Starting phenix.real_space_refine on Sat May 17 23:41:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtz_18655/05_2025/8qtz_18655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtz_18655/05_2025/8qtz_18655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qtz_18655/05_2025/8qtz_18655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtz_18655/05_2025/8qtz_18655.map" model { file = "/net/cci-nas-00/data/ceres_data/8qtz_18655/05_2025/8qtz_18655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtz_18655/05_2025/8qtz_18655.cif" } resolution = 4.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.088 sd= 0.830 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 10258 2.51 5 N 2726 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16260 Number of models: 1 Model: "" Number of chains: 3 Chain: "X" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5977 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Chain: "Y" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5977 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Chain: "Z" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4306 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY X 156 " occ=0.96 ... (2 atoms not shown) pdb=" O GLY X 156 " occ=0.96 Time building chain proxies: 8.45, per 1000 atoms: 0.52 Number of scatterers: 16260 At special positions: 0 Unit cell: (175.89, 175.89, 154.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 3224 8.00 N 2726 7.00 C 10258 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.62 Conformation dependent library (CDL) restraints added in 1.9 seconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 27 sheets defined 30.1% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'X' and resid 1 through 12 Processing helix chain 'X' and resid 15 through 26 Processing helix chain 'X' and resid 212 through 222 removed outlier: 3.662A pdb=" N CYS X 216 " --> pdb=" O GLU X 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 365 Processing helix chain 'X' and resid 494 through 510 removed outlier: 4.053A pdb=" N LEU X 498 " --> pdb=" O LEU X 494 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU X 500 " --> pdb=" O ARG X 496 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU X 503 " --> pdb=" O GLY X 499 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU X 504 " --> pdb=" O GLU X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 515 through 523 removed outlier: 3.724A pdb=" N ASP X 519 " --> pdb=" O SER X 515 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU X 522 " --> pdb=" O ILE X 518 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU X 523 " --> pdb=" O ASP X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 removed outlier: 3.728A pdb=" N PHE X 531 " --> pdb=" O MET X 527 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY X 533 " --> pdb=" O SER X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 543 through 553 Processing helix chain 'X' and resid 555 through 572 removed outlier: 3.638A pdb=" N ASN X 559 " --> pdb=" O SER X 555 " (cutoff:3.500A) Processing helix chain 'X' and resid 594 through 598 removed outlier: 3.643A pdb=" N GLN X 597 " --> pdb=" O VAL X 594 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE X 598 " --> pdb=" O SER X 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 594 through 598' Processing helix chain 'X' and resid 606 through 624 removed outlier: 3.996A pdb=" N THR X 610 " --> pdb=" O SER X 606 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN X 611 " --> pdb=" O SER X 607 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG X 618 " --> pdb=" O THR X 614 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 646 removed outlier: 3.816A pdb=" N ILE X 636 " --> pdb=" O ASN X 632 " (cutoff:3.500A) Processing helix chain 'X' and resid 655 through 667 removed outlier: 3.928A pdb=" N ILE X 659 " --> pdb=" O THR X 655 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 713 removed outlier: 3.529A pdb=" N LEU X 711 " --> pdb=" O LYS X 707 " (cutoff:3.500A) Processing helix chain 'X' and resid 723 through 731 Processing helix chain 'X' and resid 739 through 744 Processing helix chain 'X' and resid 748 through 759 removed outlier: 4.184A pdb=" N LEU X 752 " --> pdb=" O ASP X 748 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN X 758 " --> pdb=" O GLU X 754 " (cutoff:3.500A) Processing helix chain 'X' and resid 761 through 774 removed outlier: 3.869A pdb=" N ASN X 765 " --> pdb=" O PRO X 761 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 Processing helix chain 'Y' and resid 12 through 29 removed outlier: 3.861A pdb=" N ASP Y 17 " --> pdb=" O SER Y 13 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU Y 18 " --> pdb=" O TYR Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 209 through 211 No H-bonds generated for 'chain 'Y' and resid 209 through 211' Processing helix chain 'Y' and resid 212 through 222 Processing helix chain 'Y' and resid 359 through 364 removed outlier: 3.514A pdb=" N ASN Y 364 " --> pdb=" O GLN Y 360 " (cutoff:3.500A) Processing helix chain 'Y' and resid 497 through 510 removed outlier: 3.842A pdb=" N LEU Y 501 " --> pdb=" O GLN Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 521 Processing helix chain 'Y' and resid 528 through 532 Processing helix chain 'Y' and resid 540 through 553 removed outlier: 4.000A pdb=" N LYS Y 553 " --> pdb=" O MET Y 549 " (cutoff:3.500A) Processing helix chain 'Y' and resid 555 through 574 removed outlier: 3.821A pdb=" N SER Y 574 " --> pdb=" O ASP Y 570 " (cutoff:3.500A) Processing helix chain 'Y' and resid 592 through 597 removed outlier: 3.535A pdb=" N THR Y 596 " --> pdb=" O THR Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 608 through 619 Processing helix chain 'Y' and resid 620 through 625 Processing helix chain 'Y' and resid 632 through 647 removed outlier: 3.816A pdb=" N ILE Y 636 " --> pdb=" O ASN Y 632 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Y 639 " --> pdb=" O ASP Y 635 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS Y 647 " --> pdb=" O THR Y 643 " (cutoff:3.500A) Processing helix chain 'Y' and resid 652 through 654 No H-bonds generated for 'chain 'Y' and resid 652 through 654' Processing helix chain 'Y' and resid 655 through 667 removed outlier: 4.060A pdb=" N ILE Y 659 " --> pdb=" O THR Y 655 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR Y 661 " --> pdb=" O PRO Y 657 " (cutoff:3.500A) Processing helix chain 'Y' and resid 705 through 713 removed outlier: 3.799A pdb=" N THR Y 713 " --> pdb=" O ALA Y 709 " (cutoff:3.500A) Processing helix chain 'Y' and resid 723 through 734 Processing helix chain 'Y' and resid 737 through 745 Processing helix chain 'Y' and resid 748 through 758 removed outlier: 4.023A pdb=" N LEU Y 752 " --> pdb=" O ASP Y 748 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN Y 758 " --> pdb=" O GLU Y 754 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Z' and resid 2 through 12 Processing helix chain 'Z' and resid 15 through 26 removed outlier: 3.677A pdb=" N SER Z 19 " --> pdb=" O THR Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 359 through 364 removed outlier: 3.593A pdb=" N ARG Z 363 " --> pdb=" O SER Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 502 through 511 Processing helix chain 'Z' and resid 515 through 521 removed outlier: 3.504A pdb=" N ASP Z 519 " --> pdb=" O SER Z 515 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 531 removed outlier: 3.542A pdb=" N PHE Z 531 " --> pdb=" O MET Z 527 " (cutoff:3.500A) Processing helix chain 'Z' and resid 540 through 552 removed outlier: 4.622A pdb=" N MET Z 549 " --> pdb=" O ALA Z 545 " (cutoff:3.500A) Processing helix chain 'Z' and resid 553 through 555 No H-bonds generated for 'chain 'Z' and resid 553 through 555' Processing helix chain 'Z' and resid 557 through 571 Processing helix chain 'Z' and resid 607 through 624 removed outlier: 3.652A pdb=" N GLN Z 611 " --> pdb=" O SER Z 607 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET Z 624 " --> pdb=" O ARG Z 620 " (cutoff:3.500A) Processing helix chain 'Z' and resid 632 through 647 removed outlier: 3.903A pdb=" N ILE Z 636 " --> pdb=" O ASN Z 632 " (cutoff:3.500A) Processing helix chain 'Z' and resid 655 through 667 removed outlier: 4.860A pdb=" N THR Z 661 " --> pdb=" O PRO Z 657 " (cutoff:3.500A) Processing helix chain 'Z' and resid 705 through 714 removed outlier: 4.149A pdb=" N ASP Z 714 " --> pdb=" O ASP Z 710 " (cutoff:3.500A) Processing helix chain 'Z' and resid 723 through 735 Processing helix chain 'Z' and resid 737 through 746 Processing helix chain 'Z' and resid 748 through 759 removed outlier: 3.535A pdb=" N LEU Z 752 " --> pdb=" O ASP Z 748 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN Z 758 " --> pdb=" O GLU Z 754 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP Z 759 " --> pdb=" O PHE Z 755 " (cutoff:3.500A) Processing helix chain 'Z' and resid 761 through 774 removed outlier: 3.663A pdb=" N ASN Z 765 " --> pdb=" O PRO Z 761 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS Z 774 " --> pdb=" O LEU Z 770 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 49 through 50 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 49 through 50 current: chain 'X' and resid 402 through 415 removed outlier: 4.999A pdb=" N ARG X 427 " --> pdb=" O ALA X 407 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL X 409 " --> pdb=" O ARG X 425 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG X 425 " --> pdb=" O VAL X 409 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU X 411 " --> pdb=" O SER X 423 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER X 423 " --> pdb=" O LEU X 411 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR X 413 " --> pdb=" O LEU X 421 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU X 421 " --> pdb=" O THR X 413 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 420 through 432 current: chain 'Y' and resid 310 through 315 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 310 through 315 current: chain 'Y' and resid 350 through 357 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 350 through 357 current: chain 'Y' and resid 401 through 416 removed outlier: 5.146A pdb=" N LEU Y 404 " --> pdb=" O ALA Y 431 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA Y 431 " --> pdb=" O LEU Y 404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER Y 406 " --> pdb=" O ARG Y 429 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG Y 429 " --> pdb=" O SER Y 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY Y 408 " --> pdb=" O ARG Y 427 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 60 through 61 removed outlier: 6.163A pdb=" N THR X 60 " --> pdb=" O ASP Y 325 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER Y 327 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE Y 328 " --> pdb=" O SER Y 340 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER Y 340 " --> pdb=" O PHE Y 328 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY Y 330 " --> pdb=" O VAL Y 338 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL Y 338 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 73 through 74 removed outlier: 4.644A pdb=" N VAL X 93 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR X 105 " --> pdb=" O VAL X 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 80 through 83 removed outlier: 3.555A pdb=" N TYR X 206 " --> pdb=" O LEU X 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 116 through 121 removed outlier: 4.125A pdb=" N ARG X 117 " --> pdb=" O LEU X 128 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU X 128 " --> pdb=" O ARG X 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 138 through 140 removed outlier: 3.641A pdb=" N TRP X 138 " --> pdb=" O SER X 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 252 through 267 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 252 through 267 current: chain 'X' and resid 469 through 474 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 469 through 474 current: chain 'Y' and resid 462 through 474 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'X' and resid 270 through 275 Processing sheet with id=AA9, first strand: chain 'X' and resid 279 through 282 removed outlier: 9.066A pdb=" N TRP X 291 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE X 342 " --> pdb=" O TRP X 291 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU X 293 " --> pdb=" O PHE X 342 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL X 344 " --> pdb=" O GLU X 293 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N SER X 295 " --> pdb=" O VAL X 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 315 through 317 removed outlier: 3.924A pdb=" N THR X 317 " --> pdb=" O ASP X 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 320 through 321 Processing sheet with id=AB3, first strand: chain 'X' and resid 384 through 386 Processing sheet with id=AB4, first strand: chain 'X' and resid 693 through 694 removed outlier: 3.750A pdb=" N TYR X 693 " --> pdb=" O VAL X 681 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL X 681 " --> pdb=" O TYR X 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL X 675 " --> pdb=" O PHE X 682 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 33 through 34 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 33 through 34 current: chain 'Z' and resid 290 through 295 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 290 through 295 current: chain 'Z' and resid 338 through 345 Processing sheet with id=AB6, first strand: chain 'Y' and resid 81 through 82 Processing sheet with id=AB7, first strand: chain 'Y' and resid 95 through 96 removed outlier: 3.932A pdb=" N TRP Y 102 " --> pdb=" O LYS Y 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA Y 104 " --> pdb=" O VAL Y 143 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP Y 138 " --> pdb=" O LEU Y 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU Y 159 " --> pdb=" O TRP Y 138 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE Y 140 " --> pdb=" O SER Y 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 115 through 116 removed outlier: 3.554A pdb=" N VAL Y 130 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 177 through 178 Processing sheet with id=AC1, first strand: chain 'Y' and resid 278 through 281 removed outlier: 4.010A pdb=" N ALA Y 278 " --> pdb=" O LYS Y 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Y 280 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 384 through 386 Processing sheet with id=AC3, first strand: chain 'Y' and resid 680 through 685 Processing sheet with id=AC4, first strand: chain 'Z' and resid 263 through 264 removed outlier: 3.573A pdb=" N LYS Z 263 " --> pdb=" O VAL Z 474 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 271 through 273 Processing sheet with id=AC6, first strand: chain 'Z' and resid 300 through 307 removed outlier: 3.616A pdb=" N TYR Z 303 " --> pdb=" O ALA Z 314 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR Z 317 " --> pdb=" O ASP Z 354 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP Z 354 " --> pdb=" O THR Z 317 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Z 351 " --> pdb=" O PHE Z 428 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Z 428 " --> pdb=" O VAL Z 351 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU Z 421 " --> pdb=" O THR Z 413 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR Z 413 " --> pdb=" O LEU Z 421 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER Z 423 " --> pdb=" O LEU Z 411 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU Z 411 " --> pdb=" O SER Z 423 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG Z 425 " --> pdb=" O VAL Z 409 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL Z 409 " --> pdb=" O ARG Z 425 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARG Z 427 " --> pdb=" O ALA Z 407 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS Z 380 " --> pdb=" O VAL Z 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 371 through 372 removed outlier: 3.768A pdb=" N ALA Z 372 " --> pdb=" O SER Z 469 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 384 through 386 Processing sheet with id=AC9, first strand: chain 'Z' and resid 690 through 694 removed outlier: 3.867A pdb=" N PHE Z 682 " --> pdb=" O VAL Z 675 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL Z 675 " --> pdb=" O PHE Z 682 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.65 Time building geometry restraints manager: 4.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5251 1.34 - 1.46: 2833 1.46 - 1.58: 8406 1.58 - 1.70: 0 1.70 - 1.81: 91 Bond restraints: 16581 Sorted by residual: bond pdb=" N ASP Y 658 " pdb=" CA ASP Y 658 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.88e+00 bond pdb=" N ALA X 541 " pdb=" CA ALA X 541 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.25e+00 bond pdb=" N SER X 543 " pdb=" CA SER X 543 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.13e+00 bond pdb=" N SER Y 3 " pdb=" CA SER Y 3 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" N ILE Y 656 " pdb=" CA ILE Y 656 " ideal model delta sigma weight residual 1.464 1.495 -0.030 1.23e-02 6.61e+03 6.12e+00 ... (remaining 16576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 21890 2.22 - 4.44: 517 4.44 - 6.66: 98 6.66 - 8.88: 13 8.88 - 11.10: 5 Bond angle restraints: 22523 Sorted by residual: angle pdb=" C ASN Y 97 " pdb=" N ASN Y 98 " pdb=" CA ASN Y 98 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASN X 97 " pdb=" N ASN X 98 " pdb=" CA ASN X 98 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N VAL X 366 " pdb=" CA VAL X 366 " pdb=" C VAL X 366 " ideal model delta sigma weight residual 112.12 108.02 4.10 8.40e-01 1.42e+00 2.38e+01 angle pdb=" C GLN Z 393 " pdb=" N TRP Z 394 " pdb=" CA TRP Z 394 " ideal model delta sigma weight residual 120.68 128.03 -7.35 1.52e+00 4.33e-01 2.34e+01 angle pdb=" CA PRO Y 657 " pdb=" C PRO Y 657 " pdb=" O PRO Y 657 " ideal model delta sigma weight residual 121.34 116.13 5.21 1.14e+00 7.69e-01 2.09e+01 ... (remaining 22518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 8989 17.23 - 34.46: 829 34.46 - 51.68: 141 51.68 - 68.91: 23 68.91 - 86.14: 17 Dihedral angle restraints: 9999 sinusoidal: 3935 harmonic: 6064 Sorted by residual: dihedral pdb=" CA ARG Y 210 " pdb=" C ARG Y 210 " pdb=" N SER Y 211 " pdb=" CA SER Y 211 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA MET Z 549 " pdb=" C MET Z 549 " pdb=" N LYS Z 550 " pdb=" CA LYS Z 550 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" C ASP Y 658 " pdb=" N ASP Y 658 " pdb=" CA ASP Y 658 " pdb=" CB ASP Y 658 " ideal model delta harmonic sigma weight residual -122.60 -135.25 12.65 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 9996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2348 0.086 - 0.172: 216 0.172 - 0.258: 8 0.258 - 0.343: 3 0.343 - 0.429: 2 Chirality restraints: 2577 Sorted by residual: chirality pdb=" CA ASP Y 658 " pdb=" N ASP Y 658 " pdb=" C ASP Y 658 " pdb=" CB ASP Y 658 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE Z 668 " pdb=" CA ILE Z 668 " pdb=" CG1 ILE Z 668 " pdb=" CG2 ILE Z 668 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CB ILE X 55 " pdb=" CA ILE X 55 " pdb=" CG1 ILE X 55 " pdb=" CG2 ILE X 55 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2574 not shown) Planarity restraints: 2917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 356 " 0.010 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP X 356 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP X 356 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP X 356 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP X 356 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X 356 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP X 356 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 356 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 356 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP X 356 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP Y 454 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO Y 455 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO Y 455 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 455 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 224 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO Y 225 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO Y 225 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Y 225 " 0.031 5.00e-02 4.00e+02 ... (remaining 2914 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 409 2.63 - 3.20: 16486 3.20 - 3.77: 25866 3.77 - 4.33: 34000 4.33 - 4.90: 52553 Nonbonded interactions: 129314 Sorted by model distance: nonbonded pdb=" OG SER X 257 " pdb=" OE2 GLU Y 264 " model vdw 2.065 3.040 nonbonded pdb=" OG SER Y 583 " pdb=" OE1 GLN Y 597 " model vdw 2.099 3.040 nonbonded pdb=" OG SER Y 160 " pdb=" OH TYR Y 165 " model vdw 2.128 3.040 nonbonded pdb=" OG SER Y 586 " pdb=" OE1 GLN Y 706 " model vdw 2.149 3.040 nonbonded pdb=" O SER Z 292 " pdb=" OG SER Z 340 " model vdw 2.151 3.040 ... (remaining 129309 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.770 Check model and map are aligned: 0.150 Set scattering table: 0.170 Process input model: 33.470 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16581 Z= 0.187 Angle : 0.863 11.101 22523 Z= 0.479 Chirality : 0.050 0.429 2577 Planarity : 0.005 0.068 2917 Dihedral : 13.806 86.141 6077 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.00 % Favored : 88.66 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.17), residues: 2055 helix: -1.04 (0.21), residues: 525 sheet: -1.74 (0.23), residues: 483 loop : -3.52 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP X 356 HIS 0.002 0.001 HIS Y 188 PHE 0.029 0.002 PHE Y 505 TYR 0.026 0.002 TYR X 219 ARG 0.008 0.001 ARG Y 446 Details of bonding type rmsd hydrogen bonds : bond 0.21086 ( 473) hydrogen bonds : angle 8.65012 ( 1332) covalent geometry : bond 0.00368 (16581) covalent geometry : angle 0.86314 (22523) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 GLN cc_start: 0.8818 (mm110) cc_final: 0.8506 (tp-100) REVERT: X 25 ILE cc_start: 0.9111 (tp) cc_final: 0.8799 (tp) REVERT: X 31 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6607 (tm-30) REVERT: X 33 VAL cc_start: 0.7539 (t) cc_final: 0.6929 (p) REVERT: X 81 TRP cc_start: 0.6931 (m100) cc_final: 0.5851 (m100) REVERT: X 140 PHE cc_start: 0.7319 (t80) cc_final: 0.6985 (t80) REVERT: X 224 LEU cc_start: 0.8331 (tt) cc_final: 0.7992 (tt) REVERT: X 263 LYS cc_start: 0.8088 (tptt) cc_final: 0.7642 (ttmt) REVERT: X 321 ASN cc_start: 0.8145 (t0) cc_final: 0.7732 (t0) REVERT: X 367 TYR cc_start: 0.8138 (m-80) cc_final: 0.7643 (m-80) REVERT: X 375 LEU cc_start: 0.8945 (mm) cc_final: 0.8683 (mt) REVERT: X 512 ILE cc_start: 0.9218 (mm) cc_final: 0.8924 (mm) REVERT: X 575 ILE cc_start: 0.9369 (mm) cc_final: 0.8970 (mp) REVERT: X 634 ASP cc_start: 0.8670 (m-30) cc_final: 0.8461 (m-30) REVERT: X 687 ASP cc_start: 0.8218 (m-30) cc_final: 0.8016 (t0) REVERT: X 699 GLU cc_start: 0.8338 (mp0) cc_final: 0.7457 (mp0) REVERT: X 710 ASP cc_start: 0.8215 (p0) cc_final: 0.7847 (m-30) REVERT: X 718 ILE cc_start: 0.8856 (tp) cc_final: 0.8526 (tp) REVERT: X 729 ASN cc_start: 0.9071 (t0) cc_final: 0.8832 (t0) REVERT: X 770 LEU cc_start: 0.9079 (tt) cc_final: 0.8702 (tp) REVERT: X 773 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8064 (tm-30) REVERT: Y 258 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8869 (mmmm) REVERT: Y 271 ILE cc_start: 0.8830 (mm) cc_final: 0.8011 (mm) REVERT: Y 273 ILE cc_start: 0.8635 (tp) cc_final: 0.8292 (tp) REVERT: Y 328 PHE cc_start: 0.8680 (t80) cc_final: 0.8413 (t80) REVERT: Y 367 TYR cc_start: 0.8547 (m-80) cc_final: 0.8221 (m-80) REVERT: Y 460 GLU cc_start: 0.7938 (tp30) cc_final: 0.7734 (tp30) REVERT: Y 530 MET cc_start: 0.8873 (tpt) cc_final: 0.8587 (tpp) REVERT: Y 549 MET cc_start: 0.7879 (mtm) cc_final: 0.7532 (mmm) REVERT: Y 596 THR cc_start: 0.8620 (p) cc_final: 0.8404 (p) REVERT: Y 634 ASP cc_start: 0.7797 (p0) cc_final: 0.7050 (p0) REVERT: Y 643 THR cc_start: 0.9302 (m) cc_final: 0.8955 (t) REVERT: Y 645 ILE cc_start: 0.8878 (pt) cc_final: 0.8656 (pt) REVERT: Y 662 GLU cc_start: 0.8849 (pt0) cc_final: 0.8516 (pt0) REVERT: Y 673 TYR cc_start: 0.7905 (m-80) cc_final: 0.7602 (m-80) REVERT: Y 727 LEU cc_start: 0.9095 (mt) cc_final: 0.8877 (mt) REVERT: Y 743 ASN cc_start: 0.8984 (m-40) cc_final: 0.8667 (m-40) REVERT: Y 744 LEU cc_start: 0.9428 (mm) cc_final: 0.9048 (mm) REVERT: Y 753 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7769 (ttt90) REVERT: Y 765 ASN cc_start: 0.8319 (t0) cc_final: 0.8067 (t0) REVERT: Y 769 GLN cc_start: 0.7318 (mm110) cc_final: 0.6701 (mm110) REVERT: Y 773 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8440 (tm-30) REVERT: Z 1 MET cc_start: 0.8723 (tmm) cc_final: 0.8367 (tmm) REVERT: Z 271 ILE cc_start: 0.9287 (tp) cc_final: 0.8685 (tp) REVERT: Z 352 TYR cc_start: 0.8005 (m-10) cc_final: 0.7727 (m-80) REVERT: Z 422 ASN cc_start: 0.8304 (p0) cc_final: 0.8015 (p0) REVERT: Z 494 LEU cc_start: 0.8489 (mp) cc_final: 0.8190 (tt) REVERT: Z 505 PHE cc_start: 0.8186 (m-80) cc_final: 0.7528 (m-80) REVERT: Z 525 LEU cc_start: 0.8748 (pt) cc_final: 0.8428 (pp) REVERT: Z 611 GLN cc_start: 0.8767 (mp10) cc_final: 0.8395 (mp10) REVERT: Z 631 MET cc_start: 0.8215 (tmm) cc_final: 0.7863 (tmm) REVERT: Z 632 ASN cc_start: 0.8299 (t0) cc_final: 0.7503 (p0) REVERT: Z 643 THR cc_start: 0.8446 (p) cc_final: 0.8147 (p) REVERT: Z 644 LYS cc_start: 0.8507 (mmtp) cc_final: 0.8234 (mttm) REVERT: Z 659 ILE cc_start: 0.8907 (mm) cc_final: 0.8644 (tp) REVERT: Z 666 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8512 (mmmm) REVERT: Z 676 ILE cc_start: 0.8888 (mm) cc_final: 0.8617 (tp) REVERT: Z 682 PHE cc_start: 0.7559 (p90) cc_final: 0.7023 (p90) REVERT: Z 683 GLU cc_start: 0.7692 (pp20) cc_final: 0.7399 (pm20) REVERT: Z 714 ASP cc_start: 0.8386 (t0) cc_final: 0.8056 (t0) REVERT: Z 721 ILE cc_start: 0.9135 (mt) cc_final: 0.8457 (mt) REVERT: Z 728 LYS cc_start: 0.6037 (ttpt) cc_final: 0.5787 (tppt) REVERT: Z 739 GLN cc_start: 0.8097 (tp-100) cc_final: 0.6794 (tp40) REVERT: Z 748 ASP cc_start: 0.8928 (t0) cc_final: 0.8708 (t0) REVERT: Z 754 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8397 (tm-30) outliers start: 1 outliers final: 0 residues processed: 610 average time/residue: 0.2872 time to fit residues: 251.5776 Evaluate side-chains 494 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.0000 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 559 ASN X 757 ASN ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 678 ASN Y 731 ASN Z 678 ASN Z 739 GLN ** Z 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064841 restraints weight = 66070.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.066868 restraints weight = 36144.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068223 restraints weight = 22658.484| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16581 Z= 0.212 Angle : 0.787 10.411 22523 Z= 0.412 Chirality : 0.049 0.254 2577 Planarity : 0.006 0.063 2917 Dihedral : 6.038 26.829 2239 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.12 % Favored : 87.69 % Rotamer: Outliers : 0.54 % Allowed : 6.81 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.17), residues: 2055 helix: -1.13 (0.20), residues: 544 sheet: -1.64 (0.24), residues: 441 loop : -3.55 (0.16), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 356 HIS 0.002 0.001 HIS Y 170 PHE 0.041 0.002 PHE X 505 TYR 0.029 0.002 TYR Z 305 ARG 0.006 0.001 ARG Z 369 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 473) hydrogen bonds : angle 6.66701 ( 1332) covalent geometry : bond 0.00476 (16581) covalent geometry : angle 0.78719 (22523) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 526 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8855 (p0) cc_final: 0.8621 (p0) REVERT: X 81 TRP cc_start: 0.7318 (m100) cc_final: 0.5828 (m100) REVERT: X 263 LYS cc_start: 0.8415 (tptt) cc_final: 0.7955 (ttmt) REVERT: X 341 LYS cc_start: 0.7916 (tptt) cc_final: 0.7690 (tppt) REVERT: X 367 TYR cc_start: 0.8450 (m-80) cc_final: 0.7840 (m-80) REVERT: X 414 GLN cc_start: 0.8781 (tp40) cc_final: 0.8548 (tp40) REVERT: X 423 SER cc_start: 0.9195 (t) cc_final: 0.8943 (p) REVERT: X 512 ILE cc_start: 0.9145 (mm) cc_final: 0.8925 (mm) REVERT: X 530 MET cc_start: 0.8631 (ttp) cc_final: 0.8317 (ttp) REVERT: X 531 PHE cc_start: 0.9117 (m-10) cc_final: 0.8570 (m-10) REVERT: X 551 LYS cc_start: 0.9165 (ttmt) cc_final: 0.8771 (ttpt) REVERT: X 575 ILE cc_start: 0.9364 (mm) cc_final: 0.8920 (mp) REVERT: X 635 ASP cc_start: 0.8942 (m-30) cc_final: 0.8636 (m-30) REVERT: X 662 GLU cc_start: 0.8431 (pt0) cc_final: 0.7935 (pt0) REVERT: X 666 LYS cc_start: 0.9228 (mtmm) cc_final: 0.8800 (mtmm) REVERT: X 694 LYS cc_start: 0.8665 (tptp) cc_final: 0.8281 (tptt) REVERT: X 699 GLU cc_start: 0.7967 (mp0) cc_final: 0.7765 (mp0) REVERT: X 707 LYS cc_start: 0.8817 (tptp) cc_final: 0.8335 (tptp) REVERT: X 713 THR cc_start: 0.9294 (t) cc_final: 0.8931 (t) REVERT: X 718 ILE cc_start: 0.9114 (tp) cc_final: 0.8617 (tp) REVERT: X 729 ASN cc_start: 0.9182 (t0) cc_final: 0.8954 (t0) REVERT: X 762 ILE cc_start: 0.8623 (pt) cc_final: 0.8298 (pt) REVERT: X 773 GLN cc_start: 0.8532 (tm-30) cc_final: 0.8225 (tm-30) REVERT: Y 17 ASP cc_start: 0.8760 (p0) cc_final: 0.8253 (p0) REVERT: Y 107 LEU cc_start: 0.8715 (tp) cc_final: 0.7852 (tp) REVERT: Y 271 ILE cc_start: 0.8830 (mm) cc_final: 0.8195 (mm) REVERT: Y 328 PHE cc_start: 0.8519 (t80) cc_final: 0.8253 (t80) REVERT: Y 337 PHE cc_start: 0.8001 (m-80) cc_final: 0.7537 (m-80) REVERT: Y 415 PHE cc_start: 0.7847 (t80) cc_final: 0.7159 (t80) REVERT: Y 527 MET cc_start: 0.8507 (ppp) cc_final: 0.8191 (ppp) REVERT: Y 539 ASP cc_start: 0.7906 (t70) cc_final: 0.7594 (t70) REVERT: Y 549 MET cc_start: 0.7973 (mtm) cc_final: 0.7696 (mmm) REVERT: Y 566 ASP cc_start: 0.8301 (p0) cc_final: 0.8063 (p0) REVERT: Y 619 LEU cc_start: 0.8731 (mm) cc_final: 0.8081 (tp) REVERT: Y 634 ASP cc_start: 0.8024 (p0) cc_final: 0.7261 (p0) REVERT: Y 643 THR cc_start: 0.9313 (m) cc_final: 0.9092 (t) REVERT: Y 645 ILE cc_start: 0.8978 (pt) cc_final: 0.8757 (pt) REVERT: Y 662 GLU cc_start: 0.8922 (pt0) cc_final: 0.8499 (pt0) REVERT: Y 673 TYR cc_start: 0.8286 (m-80) cc_final: 0.7754 (m-10) REVERT: Y 691 PHE cc_start: 0.8862 (m-80) cc_final: 0.8245 (m-80) REVERT: Y 743 ASN cc_start: 0.9083 (m-40) cc_final: 0.8711 (m-40) REVERT: Y 745 LEU cc_start: 0.9524 (mt) cc_final: 0.9216 (mm) REVERT: Y 769 GLN cc_start: 0.7476 (mm110) cc_final: 0.7085 (tp40) REVERT: Y 773 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8480 (tm-30) REVERT: Z 1 MET cc_start: 0.8563 (tmm) cc_final: 0.8003 (tmm) REVERT: Z 5 ILE cc_start: 0.7049 (mm) cc_final: 0.6149 (mm) REVERT: Z 271 ILE cc_start: 0.9287 (tp) cc_final: 0.8558 (tp) REVERT: Z 356 TRP cc_start: 0.7455 (t-100) cc_final: 0.6484 (t-100) REVERT: Z 422 ASN cc_start: 0.8627 (p0) cc_final: 0.8330 (p0) REVERT: Z 454 ASP cc_start: 0.9019 (t70) cc_final: 0.8777 (t0) REVERT: Z 494 LEU cc_start: 0.8421 (mp) cc_final: 0.8189 (tt) REVERT: Z 505 PHE cc_start: 0.8459 (m-80) cc_final: 0.7533 (m-80) REVERT: Z 525 LEU cc_start: 0.8703 (pt) cc_final: 0.8480 (pp) REVERT: Z 611 GLN cc_start: 0.8973 (mp10) cc_final: 0.8375 (mp10) REVERT: Z 623 GLU cc_start: 0.7867 (tp30) cc_final: 0.7091 (mm-30) REVERT: Z 632 ASN cc_start: 0.8546 (t0) cc_final: 0.7956 (t0) REVERT: Z 659 ILE cc_start: 0.9043 (mm) cc_final: 0.8750 (tp) REVERT: Z 674 ARG cc_start: 0.8196 (mtm-85) cc_final: 0.7929 (mtm-85) REVERT: Z 689 LYS cc_start: 0.9193 (mmtm) cc_final: 0.8893 (mmmm) REVERT: Z 728 LYS cc_start: 0.6304 (ttpt) cc_final: 0.5989 (tppt) REVERT: Z 740 GLN cc_start: 0.9011 (mt0) cc_final: 0.8772 (mt0) REVERT: Z 748 ASP cc_start: 0.9006 (t0) cc_final: 0.8795 (t0) REVERT: Z 754 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8283 (tm-30) REVERT: Z 759 ASP cc_start: 0.8621 (p0) cc_final: 0.8293 (p0) REVERT: Z 764 ARG cc_start: 0.8047 (tpm170) cc_final: 0.6983 (tpm170) REVERT: Z 767 ILE cc_start: 0.9171 (tt) cc_final: 0.8344 (tt) outliers start: 10 outliers final: 2 residues processed: 533 average time/residue: 0.3030 time to fit residues: 232.0382 Evaluate side-chains 443 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 441 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 52 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 162 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 182 optimal weight: 0.0470 overall best weight: 1.9484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.065116 restraints weight = 65398.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.067116 restraints weight = 35976.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068461 restraints weight = 22726.693| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16581 Z= 0.173 Angle : 0.751 10.197 22523 Z= 0.393 Chirality : 0.048 0.246 2577 Planarity : 0.005 0.065 2917 Dihedral : 5.966 24.418 2239 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.19 % Favored : 88.61 % Rotamer: Outliers : 0.16 % Allowed : 4.58 % Favored : 95.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.17), residues: 2055 helix: -1.10 (0.20), residues: 544 sheet: -1.82 (0.24), residues: 435 loop : -3.47 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 356 HIS 0.003 0.001 HIS Y 436 PHE 0.040 0.002 PHE X 505 TYR 0.028 0.002 TYR X 219 ARG 0.006 0.001 ARG X 753 Details of bonding type rmsd hydrogen bonds : bond 0.04793 ( 473) hydrogen bonds : angle 6.34883 ( 1332) covalent geometry : bond 0.00391 (16581) covalent geometry : angle 0.75113 (22523) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 522 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 14 TYR cc_start: 0.7656 (p90) cc_final: 0.7445 (p90) REVERT: X 20 ASP cc_start: 0.8859 (p0) cc_final: 0.8597 (p0) REVERT: X 140 PHE cc_start: 0.7734 (t80) cc_final: 0.7132 (t80) REVERT: X 141 ILE cc_start: 0.8676 (pt) cc_final: 0.8433 (pt) REVERT: X 263 LYS cc_start: 0.8450 (tptt) cc_final: 0.8101 (ttmt) REVERT: X 276 LYS cc_start: 0.8597 (tptp) cc_final: 0.8317 (tttt) REVERT: X 341 LYS cc_start: 0.7605 (tptt) cc_final: 0.7321 (tppt) REVERT: X 367 TYR cc_start: 0.8582 (m-80) cc_final: 0.7807 (m-80) REVERT: X 423 SER cc_start: 0.9090 (t) cc_final: 0.8813 (p) REVERT: X 512 ILE cc_start: 0.9151 (mm) cc_final: 0.8920 (mm) REVERT: X 527 MET cc_start: 0.6911 (mtt) cc_final: 0.6190 (mtt) REVERT: X 531 PHE cc_start: 0.9230 (m-10) cc_final: 0.8867 (m-10) REVERT: X 551 LYS cc_start: 0.9208 (ttmt) cc_final: 0.8785 (ttpt) REVERT: X 575 ILE cc_start: 0.9360 (mm) cc_final: 0.8920 (mp) REVERT: X 615 ILE cc_start: 0.9121 (pt) cc_final: 0.8753 (pt) REVERT: X 619 LEU cc_start: 0.8504 (pp) cc_final: 0.8191 (pp) REVERT: X 635 ASP cc_start: 0.8924 (m-30) cc_final: 0.8364 (m-30) REVERT: X 658 ASP cc_start: 0.8219 (p0) cc_final: 0.7681 (p0) REVERT: X 662 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: X 665 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8596 (tm-30) REVERT: X 666 LYS cc_start: 0.9186 (mtmm) cc_final: 0.8673 (mtmm) REVERT: X 693 TYR cc_start: 0.5807 (t80) cc_final: 0.5033 (t80) REVERT: X 694 LYS cc_start: 0.8641 (tptp) cc_final: 0.8206 (tptt) REVERT: X 699 GLU cc_start: 0.8087 (mp0) cc_final: 0.7829 (mp0) REVERT: X 707 LYS cc_start: 0.8852 (tptp) cc_final: 0.8356 (tptp) REVERT: X 713 THR cc_start: 0.9204 (t) cc_final: 0.8827 (t) REVERT: X 718 ILE cc_start: 0.8989 (tp) cc_final: 0.8741 (tp) REVERT: X 729 ASN cc_start: 0.9147 (t0) cc_final: 0.8927 (t0) REVERT: X 762 ILE cc_start: 0.8238 (pt) cc_final: 0.7842 (pt) REVERT: X 773 GLN cc_start: 0.8467 (tm-30) cc_final: 0.8129 (tm-30) REVERT: Y 17 ASP cc_start: 0.8786 (p0) cc_final: 0.8352 (p0) REVERT: Y 29 LYS cc_start: 0.8833 (mmpt) cc_final: 0.8589 (tttt) REVERT: Y 107 LEU cc_start: 0.8745 (tp) cc_final: 0.7959 (tp) REVERT: Y 220 ILE cc_start: 0.7578 (tp) cc_final: 0.7204 (pt) REVERT: Y 271 ILE cc_start: 0.8694 (mm) cc_final: 0.8353 (mm) REVERT: Y 273 ILE cc_start: 0.8541 (tp) cc_final: 0.8030 (tp) REVERT: Y 328 PHE cc_start: 0.8628 (t80) cc_final: 0.8355 (t80) REVERT: Y 337 PHE cc_start: 0.7927 (m-80) cc_final: 0.7502 (m-80) REVERT: Y 415 PHE cc_start: 0.7716 (t80) cc_final: 0.7207 (t80) REVERT: Y 522 LEU cc_start: 0.9226 (tp) cc_final: 0.8995 (tp) REVERT: Y 527 MET cc_start: 0.8451 (ppp) cc_final: 0.7563 (tmm) REVERT: Y 539 ASP cc_start: 0.7971 (t70) cc_final: 0.7601 (t70) REVERT: Y 549 MET cc_start: 0.7859 (mtm) cc_final: 0.7458 (mmm) REVERT: Y 566 ASP cc_start: 0.8275 (p0) cc_final: 0.8071 (p0) REVERT: Y 619 LEU cc_start: 0.8750 (mm) cc_final: 0.8015 (tp) REVERT: Y 634 ASP cc_start: 0.8151 (p0) cc_final: 0.7437 (p0) REVERT: Y 643 THR cc_start: 0.9348 (m) cc_final: 0.9102 (t) REVERT: Y 645 ILE cc_start: 0.8983 (pt) cc_final: 0.8729 (pt) REVERT: Y 662 GLU cc_start: 0.9035 (pt0) cc_final: 0.8395 (pt0) REVERT: Y 673 TYR cc_start: 0.8138 (m-80) cc_final: 0.7536 (m-10) REVERT: Y 732 ASP cc_start: 0.7108 (t0) cc_final: 0.6733 (t70) REVERT: Y 769 GLN cc_start: 0.7232 (mm110) cc_final: 0.6805 (tp40) REVERT: Y 773 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8374 (tm-30) REVERT: Z 1 MET cc_start: 0.8741 (tmm) cc_final: 0.8000 (tmm) REVERT: Z 5 ILE cc_start: 0.6933 (mm) cc_final: 0.6036 (mm) REVERT: Z 356 TRP cc_start: 0.7328 (t-100) cc_final: 0.6806 (t-100) REVERT: Z 422 ASN cc_start: 0.8714 (p0) cc_final: 0.8504 (p0) REVERT: Z 525 LEU cc_start: 0.8876 (pt) cc_final: 0.8581 (pp) REVERT: Z 611 GLN cc_start: 0.8952 (mp10) cc_final: 0.8360 (mp10) REVERT: Z 620 ARG cc_start: 0.8152 (tmt170) cc_final: 0.7892 (tpt90) REVERT: Z 623 GLU cc_start: 0.7688 (tp30) cc_final: 0.6996 (tp30) REVERT: Z 624 MET cc_start: 0.7871 (ptp) cc_final: 0.6334 (ptp) REVERT: Z 631 MET cc_start: 0.8177 (tmm) cc_final: 0.7921 (tmm) REVERT: Z 632 ASN cc_start: 0.8662 (t0) cc_final: 0.8273 (t0) REVERT: Z 659 ILE cc_start: 0.9059 (mm) cc_final: 0.8708 (tp) REVERT: Z 666 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8803 (mppt) REVERT: Z 689 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8881 (mmmm) REVERT: Z 721 ILE cc_start: 0.9420 (mt) cc_final: 0.8672 (mt) REVERT: Z 728 LYS cc_start: 0.6252 (ttpt) cc_final: 0.6044 (tppt) REVERT: Z 754 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8258 (tm-30) REVERT: Z 759 ASP cc_start: 0.8547 (p0) cc_final: 0.8245 (p0) REVERT: Z 764 ARG cc_start: 0.8073 (tpm170) cc_final: 0.6877 (tpm170) REVERT: Z 767 ILE cc_start: 0.9175 (tt) cc_final: 0.8506 (tt) outliers start: 3 outliers final: 0 residues processed: 523 average time/residue: 0.3021 time to fit residues: 228.1264 Evaluate side-chains 453 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 126 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 149 optimal weight: 0.0980 chunk 148 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 15 optimal weight: 20.0000 chunk 158 optimal weight: 0.0170 chunk 183 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.0224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 324 ASN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 678 ASN Z 773 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.078754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.066477 restraints weight = 64596.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.068508 restraints weight = 35319.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.069905 restraints weight = 22294.340| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16581 Z= 0.141 Angle : 0.736 10.080 22523 Z= 0.381 Chirality : 0.048 0.220 2577 Planarity : 0.005 0.085 2917 Dihedral : 5.786 24.602 2239 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.24 % Favored : 88.56 % Rotamer: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.48 (0.17), residues: 2055 helix: -0.99 (0.21), residues: 545 sheet: -1.65 (0.24), residues: 448 loop : -3.45 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 356 HIS 0.002 0.001 HIS Y 436 PHE 0.046 0.002 PHE X 505 TYR 0.022 0.001 TYR Z 461 ARG 0.008 0.001 ARG Z 502 Details of bonding type rmsd hydrogen bonds : bond 0.04402 ( 473) hydrogen bonds : angle 6.13706 ( 1332) covalent geometry : bond 0.00318 (16581) covalent geometry : angle 0.73648 (22523) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 520 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8805 (p0) cc_final: 0.8568 (p0) REVERT: X 21 GLU cc_start: 0.8441 (pp20) cc_final: 0.7844 (pp20) REVERT: X 22 ILE cc_start: 0.8925 (mm) cc_final: 0.8591 (mm) REVERT: X 25 ILE cc_start: 0.8686 (tp) cc_final: 0.8466 (tp) REVERT: X 81 TRP cc_start: 0.7222 (m100) cc_final: 0.5868 (m100) REVERT: X 140 PHE cc_start: 0.7345 (t80) cc_final: 0.6876 (t80) REVERT: X 141 ILE cc_start: 0.8529 (pt) cc_final: 0.8322 (pt) REVERT: X 142 ASP cc_start: 0.6146 (m-30) cc_final: 0.5348 (m-30) REVERT: X 263 LYS cc_start: 0.8338 (tptt) cc_final: 0.8025 (ttmt) REVERT: X 367 TYR cc_start: 0.8567 (m-80) cc_final: 0.7839 (m-80) REVERT: X 371 LEU cc_start: 0.7795 (pt) cc_final: 0.7371 (pt) REVERT: X 375 LEU cc_start: 0.8902 (mm) cc_final: 0.8610 (mt) REVERT: X 423 SER cc_start: 0.9186 (t) cc_final: 0.8887 (p) REVERT: X 511 GLU cc_start: 0.8848 (pp20) cc_final: 0.8628 (tm-30) REVERT: X 527 MET cc_start: 0.6885 (mtt) cc_final: 0.6668 (mtt) REVERT: X 551 LYS cc_start: 0.9075 (ttmt) cc_final: 0.8760 (ttpt) REVERT: X 631 MET cc_start: 0.8646 (tpp) cc_final: 0.8267 (tpp) REVERT: X 635 ASP cc_start: 0.8929 (m-30) cc_final: 0.8428 (m-30) REVERT: X 644 LYS cc_start: 0.8806 (tppt) cc_final: 0.8442 (mmmm) REVERT: X 658 ASP cc_start: 0.8262 (p0) cc_final: 0.8050 (p0) REVERT: X 665 GLU cc_start: 0.8800 (tm-30) cc_final: 0.8462 (tm-30) REVERT: X 666 LYS cc_start: 0.9139 (mtmm) cc_final: 0.8571 (mtmm) REVERT: X 694 LYS cc_start: 0.8625 (tptp) cc_final: 0.8254 (tptt) REVERT: X 699 GLU cc_start: 0.8072 (mp0) cc_final: 0.7785 (mp0) REVERT: X 703 PHE cc_start: 0.7452 (p90) cc_final: 0.6274 (p90) REVERT: X 707 LYS cc_start: 0.8851 (tptp) cc_final: 0.8536 (tptp) REVERT: X 718 ILE cc_start: 0.9094 (tp) cc_final: 0.8545 (tp) REVERT: X 729 ASN cc_start: 0.9114 (t0) cc_final: 0.8897 (t0) REVERT: X 762 ILE cc_start: 0.8426 (pt) cc_final: 0.8012 (pt) REVERT: X 773 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8312 (tm-30) REVERT: Y 17 ASP cc_start: 0.8857 (p0) cc_final: 0.8442 (p0) REVERT: Y 29 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8461 (tttt) REVERT: Y 107 LEU cc_start: 0.8777 (tp) cc_final: 0.8020 (tp) REVERT: Y 220 ILE cc_start: 0.7574 (tp) cc_final: 0.7198 (pt) REVERT: Y 271 ILE cc_start: 0.8746 (mm) cc_final: 0.8480 (mm) REVERT: Y 273 ILE cc_start: 0.8616 (tp) cc_final: 0.8073 (tp) REVERT: Y 328 PHE cc_start: 0.8660 (t80) cc_final: 0.8378 (t80) REVERT: Y 380 CYS cc_start: 0.8719 (m) cc_final: 0.8181 (t) REVERT: Y 415 PHE cc_start: 0.7561 (t80) cc_final: 0.7091 (t80) REVERT: Y 522 LEU cc_start: 0.9216 (tp) cc_final: 0.8964 (tp) REVERT: Y 527 MET cc_start: 0.8447 (ppp) cc_final: 0.7656 (tmm) REVERT: Y 539 ASP cc_start: 0.7964 (t70) cc_final: 0.7614 (t70) REVERT: Y 549 MET cc_start: 0.7857 (mtm) cc_final: 0.7393 (mmm) REVERT: Y 619 LEU cc_start: 0.8741 (mm) cc_final: 0.7975 (tp) REVERT: Y 634 ASP cc_start: 0.7736 (p0) cc_final: 0.7161 (p0) REVERT: Y 643 THR cc_start: 0.9358 (m) cc_final: 0.9103 (t) REVERT: Y 662 GLU cc_start: 0.8915 (pt0) cc_final: 0.8316 (pt0) REVERT: Y 673 TYR cc_start: 0.8122 (m-80) cc_final: 0.7529 (m-10) REVERT: Y 680 ASP cc_start: 0.7948 (m-30) cc_final: 0.7599 (m-30) REVERT: Y 691 PHE cc_start: 0.8650 (m-80) cc_final: 0.8378 (m-80) REVERT: Y 743 ASN cc_start: 0.8793 (m-40) cc_final: 0.8592 (m-40) REVERT: Y 769 GLN cc_start: 0.7481 (mm110) cc_final: 0.7094 (tp40) REVERT: Y 773 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8276 (tm-30) REVERT: Z 1 MET cc_start: 0.8603 (tmm) cc_final: 0.7710 (tmm) REVERT: Z 5 ILE cc_start: 0.6859 (mm) cc_final: 0.6078 (mm) REVERT: Z 271 ILE cc_start: 0.9378 (tp) cc_final: 0.8775 (tp) REVERT: Z 273 ILE cc_start: 0.9181 (tp) cc_final: 0.8880 (tp) REVERT: Z 356 TRP cc_start: 0.7257 (t-100) cc_final: 0.6907 (t-100) REVERT: Z 497 GLN cc_start: 0.7517 (mp10) cc_final: 0.7108 (mp10) REVERT: Z 505 PHE cc_start: 0.8529 (m-80) cc_final: 0.7817 (m-80) REVERT: Z 611 GLN cc_start: 0.8974 (mp10) cc_final: 0.8408 (mp10) REVERT: Z 623 GLU cc_start: 0.7675 (tp30) cc_final: 0.6752 (mm-30) REVERT: Z 632 ASN cc_start: 0.8627 (t0) cc_final: 0.8139 (t0) REVERT: Z 662 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7269 (mp0) REVERT: Z 683 GLU cc_start: 0.7637 (pp20) cc_final: 0.7247 (pp20) REVERT: Z 689 LYS cc_start: 0.9105 (mmtm) cc_final: 0.8784 (mmmm) REVERT: Z 721 ILE cc_start: 0.9435 (mt) cc_final: 0.9199 (mp) REVERT: Z 728 LYS cc_start: 0.6215 (ttpt) cc_final: 0.5836 (tppt) REVERT: Z 748 ASP cc_start: 0.8989 (t0) cc_final: 0.8745 (t0) REVERT: Z 754 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8217 (tm-30) REVERT: Z 759 ASP cc_start: 0.8504 (p0) cc_final: 0.8167 (p0) REVERT: Z 764 ARG cc_start: 0.8025 (tpm170) cc_final: 0.6859 (tpm170) REVERT: Z 767 ILE cc_start: 0.9162 (tt) cc_final: 0.8510 (tt) outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.2799 time to fit residues: 211.0263 Evaluate side-chains 449 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 37 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 152 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 757 ASN ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 266 GLN Z 760 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.064999 restraints weight = 66223.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.067022 restraints weight = 36272.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068393 restraints weight = 22797.111| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3130 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16581 Z= 0.172 Angle : 0.753 10.295 22523 Z= 0.390 Chirality : 0.047 0.266 2577 Planarity : 0.006 0.074 2917 Dihedral : 5.848 25.936 2239 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.07 % Favored : 87.79 % Rotamer: Outliers : 0.05 % Allowed : 3.38 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.17), residues: 2055 helix: -1.01 (0.21), residues: 546 sheet: -1.59 (0.23), residues: 478 loop : -3.46 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 356 HIS 0.002 0.001 HIS X 188 PHE 0.038 0.002 PHE X 724 TYR 0.023 0.002 TYR Z 461 ARG 0.005 0.001 ARG Z 502 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 473) hydrogen bonds : angle 6.06004 ( 1332) covalent geometry : bond 0.00387 (16581) covalent geometry : angle 0.75282 (22523) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 504 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8839 (p0) cc_final: 0.8574 (p0) REVERT: X 21 GLU cc_start: 0.8666 (pp20) cc_final: 0.8350 (pp20) REVERT: X 25 ILE cc_start: 0.8680 (tp) cc_final: 0.8373 (tp) REVERT: X 81 TRP cc_start: 0.7476 (m100) cc_final: 0.6040 (m100) REVERT: X 140 PHE cc_start: 0.7373 (t80) cc_final: 0.7100 (t80) REVERT: X 263 LYS cc_start: 0.8402 (tptt) cc_final: 0.8197 (ttmt) REVERT: X 371 LEU cc_start: 0.7719 (pt) cc_final: 0.7268 (pt) REVERT: X 423 SER cc_start: 0.9211 (t) cc_final: 0.8934 (p) REVERT: X 512 ILE cc_start: 0.9396 (mm) cc_final: 0.9123 (mm) REVERT: X 530 MET cc_start: 0.8947 (tpt) cc_final: 0.8670 (tpp) REVERT: X 531 PHE cc_start: 0.9150 (m-10) cc_final: 0.8561 (m-10) REVERT: X 544 MET cc_start: 0.8972 (ppp) cc_final: 0.8314 (ppp) REVERT: X 551 LYS cc_start: 0.9077 (ttmt) cc_final: 0.8787 (ttpt) REVERT: X 623 GLU cc_start: 0.7467 (mp0) cc_final: 0.7263 (mp0) REVERT: X 658 ASP cc_start: 0.8393 (p0) cc_final: 0.8171 (p0) REVERT: X 665 GLU cc_start: 0.8784 (tm-30) cc_final: 0.8469 (tm-30) REVERT: X 666 LYS cc_start: 0.9146 (mtmm) cc_final: 0.8557 (mtmm) REVERT: X 694 LYS cc_start: 0.8656 (tptp) cc_final: 0.8193 (tptt) REVERT: X 699 GLU cc_start: 0.8174 (mp0) cc_final: 0.7958 (mp0) REVERT: X 704 ASP cc_start: 0.8316 (t70) cc_final: 0.8046 (t0) REVERT: X 707 LYS cc_start: 0.8905 (tptp) cc_final: 0.8574 (tptp) REVERT: X 768 GLU cc_start: 0.8559 (tm-30) cc_final: 0.8316 (tm-30) REVERT: X 769 GLN cc_start: 0.8544 (pp30) cc_final: 0.8323 (pp30) REVERT: X 773 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8331 (tm-30) REVERT: Y 9 LEU cc_start: 0.8957 (mt) cc_final: 0.8735 (mt) REVERT: Y 12 ASN cc_start: 0.7998 (m-40) cc_final: 0.7752 (m-40) REVERT: Y 17 ASP cc_start: 0.8710 (p0) cc_final: 0.8266 (p0) REVERT: Y 107 LEU cc_start: 0.8730 (tp) cc_final: 0.8167 (tp) REVERT: Y 220 ILE cc_start: 0.7598 (tp) cc_final: 0.7248 (pt) REVERT: Y 273 ILE cc_start: 0.8693 (tp) cc_final: 0.8157 (tp) REVERT: Y 328 PHE cc_start: 0.8543 (t80) cc_final: 0.8294 (t80) REVERT: Y 344 VAL cc_start: 0.8835 (t) cc_final: 0.8549 (t) REVERT: Y 380 CYS cc_start: 0.8598 (m) cc_final: 0.8302 (m) REVERT: Y 415 PHE cc_start: 0.7633 (t80) cc_final: 0.7164 (t80) REVERT: Y 471 ILE cc_start: 0.9510 (tp) cc_final: 0.9210 (tp) REVERT: Y 514 MET cc_start: 0.7429 (ptm) cc_final: 0.7188 (ptm) REVERT: Y 519 ASP cc_start: 0.7602 (m-30) cc_final: 0.7115 (m-30) REVERT: Y 522 LEU cc_start: 0.9280 (tp) cc_final: 0.9059 (tp) REVERT: Y 527 MET cc_start: 0.8437 (ppp) cc_final: 0.7669 (tmm) REVERT: Y 539 ASP cc_start: 0.8076 (t70) cc_final: 0.7755 (t70) REVERT: Y 549 MET cc_start: 0.7880 (mtm) cc_final: 0.7452 (tmm) REVERT: Y 619 LEU cc_start: 0.8828 (mm) cc_final: 0.8113 (tp) REVERT: Y 634 ASP cc_start: 0.8110 (p0) cc_final: 0.7454 (p0) REVERT: Y 645 ILE cc_start: 0.9035 (pt) cc_final: 0.8804 (pt) REVERT: Y 662 GLU cc_start: 0.8931 (pt0) cc_final: 0.8353 (pt0) REVERT: Y 673 TYR cc_start: 0.8190 (m-80) cc_final: 0.7691 (m-10) REVERT: Y 691 PHE cc_start: 0.8954 (m-80) cc_final: 0.8303 (m-80) REVERT: Y 769 GLN cc_start: 0.7216 (mm110) cc_final: 0.6692 (tp40) REVERT: Y 773 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8357 (tm-30) REVERT: Z 1 MET cc_start: 0.8718 (tmm) cc_final: 0.7784 (tmm) REVERT: Z 5 ILE cc_start: 0.6044 (mm) cc_final: 0.5647 (mm) REVERT: Z 8 GLN cc_start: 0.8013 (pm20) cc_final: 0.7444 (pm20) REVERT: Z 263 LYS cc_start: 0.9189 (mppt) cc_final: 0.8914 (mmtm) REVERT: Z 271 ILE cc_start: 0.9429 (tp) cc_final: 0.8833 (tp) REVERT: Z 276 LYS cc_start: 0.8971 (tptm) cc_final: 0.8440 (ttmm) REVERT: Z 293 GLU cc_start: 0.7942 (pp20) cc_final: 0.7696 (tm-30) REVERT: Z 371 LEU cc_start: 0.9189 (tp) cc_final: 0.8882 (tp) REVERT: Z 505 PHE cc_start: 0.8606 (m-80) cc_final: 0.7921 (m-80) REVERT: Z 611 GLN cc_start: 0.9033 (mp10) cc_final: 0.8425 (mp10) REVERT: Z 623 GLU cc_start: 0.7474 (tp30) cc_final: 0.6840 (mm-30) REVERT: Z 631 MET cc_start: 0.8019 (tmm) cc_final: 0.7794 (tmm) REVERT: Z 662 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7208 (mp0) REVERT: Z 683 GLU cc_start: 0.7806 (pp20) cc_final: 0.7027 (pp20) REVERT: Z 689 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8862 (mmmm) REVERT: Z 721 ILE cc_start: 0.9425 (mt) cc_final: 0.8666 (mt) REVERT: Z 728 LYS cc_start: 0.6284 (ttpt) cc_final: 0.6054 (tppt) REVERT: Z 753 ARG cc_start: 0.8716 (tmm-80) cc_final: 0.8491 (ttp80) REVERT: Z 759 ASP cc_start: 0.8547 (p0) cc_final: 0.8021 (p0) REVERT: Z 760 ASN cc_start: 0.7730 (OUTLIER) cc_final: 0.7467 (m110) REVERT: Z 764 ARG cc_start: 0.7636 (tpm170) cc_final: 0.7251 (tpm170) REVERT: Z 767 ILE cc_start: 0.9124 (tt) cc_final: 0.8752 (tt) outliers start: 1 outliers final: 0 residues processed: 505 average time/residue: 0.2766 time to fit residues: 203.6308 Evaluate side-chains 443 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 24 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 178 optimal weight: 0.1980 chunk 144 optimal weight: 3.9990 chunk 204 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 757 ASN ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.076786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064523 restraints weight = 65534.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066537 restraints weight = 36017.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.067911 restraints weight = 22665.992| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16581 Z= 0.191 Angle : 0.771 12.037 22523 Z= 0.400 Chirality : 0.049 0.456 2577 Planarity : 0.006 0.149 2917 Dihedral : 5.905 26.856 2239 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.17 % Favored : 87.69 % Rotamer: Outliers : 0.05 % Allowed : 2.72 % Favored : 97.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.46 (0.17), residues: 2055 helix: -0.97 (0.21), residues: 550 sheet: -1.68 (0.23), residues: 462 loop : -3.44 (0.17), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 356 HIS 0.003 0.001 HIS X 188 PHE 0.079 0.002 PHE X 724 TYR 0.026 0.002 TYR Z 305 ARG 0.027 0.001 ARG X 674 Details of bonding type rmsd hydrogen bonds : bond 0.04529 ( 473) hydrogen bonds : angle 6.02066 ( 1332) covalent geometry : bond 0.00431 (16581) covalent geometry : angle 0.77143 (22523) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 503 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8836 (p0) cc_final: 0.8600 (p0) REVERT: X 21 GLU cc_start: 0.8658 (pp20) cc_final: 0.8325 (pp20) REVERT: X 25 ILE cc_start: 0.8678 (tp) cc_final: 0.8341 (tp) REVERT: X 81 TRP cc_start: 0.7398 (m100) cc_final: 0.5790 (m100) REVERT: X 140 PHE cc_start: 0.7414 (t80) cc_final: 0.7055 (t80) REVERT: X 263 LYS cc_start: 0.8465 (tptt) cc_final: 0.8232 (ttmt) REVERT: X 371 LEU cc_start: 0.7769 (pt) cc_final: 0.7384 (pt) REVERT: X 375 LEU cc_start: 0.8878 (mm) cc_final: 0.8604 (mt) REVERT: X 423 SER cc_start: 0.9071 (t) cc_final: 0.8814 (p) REVERT: X 511 GLU cc_start: 0.8839 (pp20) cc_final: 0.8638 (tm-30) REVERT: X 512 ILE cc_start: 0.9278 (mm) cc_final: 0.9039 (mm) REVERT: X 527 MET cc_start: 0.7200 (mtt) cc_final: 0.6770 (mtt) REVERT: X 551 LYS cc_start: 0.9026 (ttmt) cc_final: 0.8729 (ttpt) REVERT: X 635 ASP cc_start: 0.8693 (m-30) cc_final: 0.8218 (m-30) REVERT: X 662 GLU cc_start: 0.8265 (pm20) cc_final: 0.7748 (pm20) REVERT: X 665 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8438 (tm-30) REVERT: X 666 LYS cc_start: 0.9098 (mtmm) cc_final: 0.8539 (mtmm) REVERT: X 694 LYS cc_start: 0.8653 (tptp) cc_final: 0.8220 (tptt) REVERT: X 699 GLU cc_start: 0.8163 (mp0) cc_final: 0.7896 (mp0) REVERT: X 704 ASP cc_start: 0.8378 (t70) cc_final: 0.7988 (t0) REVERT: X 768 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8366 (tm-30) REVERT: Y 4 LEU cc_start: 0.7204 (pt) cc_final: 0.6270 (pt) REVERT: Y 8 GLN cc_start: 0.8252 (mp10) cc_final: 0.7954 (mp10) REVERT: Y 9 LEU cc_start: 0.8826 (mt) cc_final: 0.8623 (mt) REVERT: Y 17 ASP cc_start: 0.8810 (p0) cc_final: 0.8394 (p0) REVERT: Y 107 LEU cc_start: 0.8706 (tp) cc_final: 0.8291 (tp) REVERT: Y 220 ILE cc_start: 0.7695 (tp) cc_final: 0.7133 (pt) REVERT: Y 273 ILE cc_start: 0.8720 (tp) cc_final: 0.8029 (tp) REVERT: Y 328 PHE cc_start: 0.8573 (t80) cc_final: 0.8291 (t80) REVERT: Y 337 PHE cc_start: 0.8018 (m-80) cc_final: 0.7638 (m-80) REVERT: Y 342 PHE cc_start: 0.7384 (t80) cc_final: 0.7175 (t80) REVERT: Y 380 CYS cc_start: 0.8519 (m) cc_final: 0.8258 (m) REVERT: Y 415 PHE cc_start: 0.7595 (t80) cc_final: 0.7223 (t80) REVERT: Y 471 ILE cc_start: 0.9536 (tp) cc_final: 0.9266 (tp) REVERT: Y 519 ASP cc_start: 0.7595 (m-30) cc_final: 0.7088 (m-30) REVERT: Y 527 MET cc_start: 0.8420 (ppp) cc_final: 0.7856 (tmm) REVERT: Y 539 ASP cc_start: 0.8029 (t70) cc_final: 0.7790 (t70) REVERT: Y 547 ASN cc_start: 0.8916 (m110) cc_final: 0.8683 (m-40) REVERT: Y 549 MET cc_start: 0.7890 (mtm) cc_final: 0.7403 (tmm) REVERT: Y 619 LEU cc_start: 0.8805 (mm) cc_final: 0.8034 (tp) REVERT: Y 634 ASP cc_start: 0.7925 (p0) cc_final: 0.7348 (p0) REVERT: Y 662 GLU cc_start: 0.8925 (pt0) cc_final: 0.8326 (pt0) REVERT: Y 673 TYR cc_start: 0.8206 (m-80) cc_final: 0.7703 (m-10) REVERT: Y 691 PHE cc_start: 0.8903 (m-80) cc_final: 0.8252 (m-80) REVERT: Y 769 GLN cc_start: 0.7190 (mm110) cc_final: 0.6740 (tp40) REVERT: Y 773 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8233 (tm-30) REVERT: Z 1 MET cc_start: 0.8726 (tmm) cc_final: 0.8379 (tmm) REVERT: Z 5 ILE cc_start: 0.6866 (mm) cc_final: 0.6169 (mm) REVERT: Z 263 LYS cc_start: 0.9125 (mppt) cc_final: 0.8898 (mmtm) REVERT: Z 265 MET cc_start: 0.8459 (mmp) cc_final: 0.8241 (mmp) REVERT: Z 271 ILE cc_start: 0.9364 (tp) cc_final: 0.8710 (tp) REVERT: Z 273 ILE cc_start: 0.9057 (tp) cc_final: 0.8845 (tp) REVERT: Z 276 LYS cc_start: 0.8990 (tptm) cc_final: 0.8408 (ttmm) REVERT: Z 371 LEU cc_start: 0.9234 (tp) cc_final: 0.8876 (tp) REVERT: Z 425 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7883 (mtp85) REVERT: Z 528 PHE cc_start: 0.8772 (t80) cc_final: 0.8340 (t80) REVERT: Z 611 GLN cc_start: 0.9050 (mp10) cc_final: 0.8462 (mp10) REVERT: Z 623 GLU cc_start: 0.7495 (tp30) cc_final: 0.6903 (mm-30) REVERT: Z 632 ASN cc_start: 0.8272 (t0) cc_final: 0.7606 (p0) REVERT: Z 674 ARG cc_start: 0.9064 (ptp-110) cc_final: 0.8403 (ptp90) REVERT: Z 689 LYS cc_start: 0.9230 (mmtm) cc_final: 0.9000 (mmmm) REVERT: Z 728 LYS cc_start: 0.6291 (ttpt) cc_final: 0.6058 (tppt) REVERT: Z 753 ARG cc_start: 0.8759 (tmm-80) cc_final: 0.8479 (ttp80) REVERT: Z 759 ASP cc_start: 0.8411 (p0) cc_final: 0.8089 (p0) REVERT: Z 764 ARG cc_start: 0.7810 (tpm170) cc_final: 0.7230 (tpm170) REVERT: Z 767 ILE cc_start: 0.9110 (tt) cc_final: 0.8670 (tt) outliers start: 1 outliers final: 0 residues processed: 504 average time/residue: 0.2977 time to fit residues: 219.2768 Evaluate side-chains 433 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 433 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 757 ASN ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 739 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.076835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.064482 restraints weight = 65403.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.066490 restraints weight = 36011.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.067842 restraints weight = 22701.209| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16581 Z= 0.177 Angle : 0.763 10.409 22523 Z= 0.394 Chirality : 0.049 0.351 2577 Planarity : 0.006 0.105 2917 Dihedral : 5.879 26.372 2239 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 17.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.36 % Favored : 87.49 % Rotamer: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.17), residues: 2055 helix: -0.97 (0.21), residues: 550 sheet: -1.78 (0.23), residues: 490 loop : -3.40 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 356 HIS 0.003 0.001 HIS X 188 PHE 0.030 0.002 PHE Y 505 TYR 0.026 0.002 TYR Z 461 ARG 0.011 0.001 ARG X 618 Details of bonding type rmsd hydrogen bonds : bond 0.04478 ( 473) hydrogen bonds : angle 5.95064 ( 1332) covalent geometry : bond 0.00406 (16581) covalent geometry : angle 0.76337 (22523) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8801 (p0) cc_final: 0.8549 (p0) REVERT: X 21 GLU cc_start: 0.8662 (pp20) cc_final: 0.8196 (tm-30) REVERT: X 25 ILE cc_start: 0.8633 (tp) cc_final: 0.8191 (tp) REVERT: X 81 TRP cc_start: 0.7324 (m100) cc_final: 0.5639 (m100) REVERT: X 140 PHE cc_start: 0.7363 (t80) cc_final: 0.7027 (t80) REVERT: X 423 SER cc_start: 0.9093 (t) cc_final: 0.8792 (p) REVERT: X 508 LEU cc_start: 0.9475 (pp) cc_final: 0.9117 (pp) REVERT: X 527 MET cc_start: 0.7294 (mtt) cc_final: 0.6744 (mtt) REVERT: X 530 MET cc_start: 0.8916 (tpt) cc_final: 0.8656 (tpp) REVERT: X 551 LYS cc_start: 0.9083 (ttmt) cc_final: 0.8748 (ttpt) REVERT: X 631 MET cc_start: 0.8783 (tpp) cc_final: 0.8299 (tpp) REVERT: X 644 LYS cc_start: 0.8658 (tttt) cc_final: 0.8075 (mmmt) REVERT: X 645 ILE cc_start: 0.9289 (tp) cc_final: 0.9001 (pt) REVERT: X 662 GLU cc_start: 0.8152 (pm20) cc_final: 0.7656 (pm20) REVERT: X 665 GLU cc_start: 0.8869 (tm-30) cc_final: 0.8540 (tm-30) REVERT: X 666 LYS cc_start: 0.9074 (mtmm) cc_final: 0.8546 (mtmm) REVERT: X 673 TYR cc_start: 0.8474 (m-80) cc_final: 0.8178 (m-80) REVERT: X 694 LYS cc_start: 0.8693 (tptp) cc_final: 0.8277 (tptt) REVERT: X 699 GLU cc_start: 0.8166 (mp0) cc_final: 0.7881 (mp0) REVERT: X 704 ASP cc_start: 0.8386 (t70) cc_final: 0.8009 (t0) REVERT: X 707 LYS cc_start: 0.9039 (tptp) cc_final: 0.8583 (tptp) REVERT: X 714 ASP cc_start: 0.8676 (p0) cc_final: 0.8199 (p0) REVERT: X 718 ILE cc_start: 0.9118 (tp) cc_final: 0.8630 (tp) REVERT: Y 9 LEU cc_start: 0.8839 (mt) cc_final: 0.8604 (mt) REVERT: Y 17 ASP cc_start: 0.8836 (p0) cc_final: 0.8334 (p0) REVERT: Y 107 LEU cc_start: 0.8816 (tp) cc_final: 0.8500 (tp) REVERT: Y 220 ILE cc_start: 0.7566 (tp) cc_final: 0.7310 (pt) REVERT: Y 277 PHE cc_start: 0.6838 (t80) cc_final: 0.6634 (t80) REVERT: Y 328 PHE cc_start: 0.8687 (t80) cc_final: 0.8376 (t80) REVERT: Y 337 PHE cc_start: 0.8001 (m-80) cc_final: 0.7564 (m-80) REVERT: Y 342 PHE cc_start: 0.7347 (t80) cc_final: 0.7089 (t80) REVERT: Y 380 CYS cc_start: 0.8455 (m) cc_final: 0.8181 (m) REVERT: Y 415 PHE cc_start: 0.7634 (t80) cc_final: 0.7270 (t80) REVERT: Y 471 ILE cc_start: 0.9507 (tp) cc_final: 0.9202 (tp) REVERT: Y 519 ASP cc_start: 0.7715 (m-30) cc_final: 0.7151 (m-30) REVERT: Y 522 LEU cc_start: 0.9307 (tp) cc_final: 0.9104 (tp) REVERT: Y 527 MET cc_start: 0.8456 (ppp) cc_final: 0.7671 (tmm) REVERT: Y 539 ASP cc_start: 0.8015 (t70) cc_final: 0.7805 (t70) REVERT: Y 549 MET cc_start: 0.8059 (mtm) cc_final: 0.7626 (tmm) REVERT: Y 619 LEU cc_start: 0.8754 (mm) cc_final: 0.7995 (tp) REVERT: Y 634 ASP cc_start: 0.7822 (p0) cc_final: 0.7345 (p0) REVERT: Y 662 GLU cc_start: 0.8944 (pt0) cc_final: 0.8371 (pt0) REVERT: Y 673 TYR cc_start: 0.8162 (m-80) cc_final: 0.7635 (m-10) REVERT: Y 680 ASP cc_start: 0.7908 (m-30) cc_final: 0.7602 (m-30) REVERT: Y 691 PHE cc_start: 0.8836 (m-80) cc_final: 0.8299 (m-80) REVERT: Y 724 PHE cc_start: 0.7089 (m-80) cc_final: 0.6128 (m-80) REVERT: Y 726 THR cc_start: 0.8527 (p) cc_final: 0.8314 (p) REVERT: Y 732 ASP cc_start: 0.7020 (t0) cc_final: 0.6692 (t70) REVERT: Y 750 ARG cc_start: 0.8353 (ttm110) cc_final: 0.8142 (ttm110) REVERT: Y 769 GLN cc_start: 0.7198 (mm110) cc_final: 0.6750 (tp40) REVERT: Y 773 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8221 (tm-30) REVERT: Z 5 ILE cc_start: 0.7043 (mm) cc_final: 0.6375 (mm) REVERT: Z 8 GLN cc_start: 0.8139 (pm20) cc_final: 0.7862 (pm20) REVERT: Z 21 GLU cc_start: 0.8448 (tt0) cc_final: 0.7660 (tm-30) REVERT: Z 263 LYS cc_start: 0.9254 (mppt) cc_final: 0.8827 (mmtm) REVERT: Z 271 ILE cc_start: 0.9241 (tp) cc_final: 0.8975 (tp) REVERT: Z 276 LYS cc_start: 0.9042 (tptm) cc_final: 0.8461 (ttmm) REVERT: Z 357 ASP cc_start: 0.8247 (m-30) cc_final: 0.7468 (m-30) REVERT: Z 371 LEU cc_start: 0.9220 (tp) cc_final: 0.8871 (tp) REVERT: Z 425 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7925 (mtp85) REVERT: Z 497 GLN cc_start: 0.7867 (mp10) cc_final: 0.7462 (mp10) REVERT: Z 528 PHE cc_start: 0.8752 (t80) cc_final: 0.8349 (t80) REVERT: Z 611 GLN cc_start: 0.9044 (mp10) cc_final: 0.8474 (mp10) REVERT: Z 624 MET cc_start: 0.7573 (ptp) cc_final: 0.5987 (ptp) REVERT: Z 632 ASN cc_start: 0.8291 (t0) cc_final: 0.7869 (p0) REVERT: Z 662 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7312 (mp0) REVERT: Z 674 ARG cc_start: 0.9033 (ptp-110) cc_final: 0.8424 (ptp90) REVERT: Z 689 LYS cc_start: 0.9264 (mmtm) cc_final: 0.9060 (mmmm) REVERT: Z 728 LYS cc_start: 0.6331 (ttpt) cc_final: 0.5915 (tppt) REVERT: Z 748 ASP cc_start: 0.8995 (t0) cc_final: 0.8766 (t0) REVERT: Z 753 ARG cc_start: 0.8777 (tmm-80) cc_final: 0.8359 (ttp80) REVERT: Z 759 ASP cc_start: 0.8438 (p0) cc_final: 0.8030 (p0) outliers start: 0 outliers final: 0 residues processed: 502 average time/residue: 0.2878 time to fit residues: 210.2233 Evaluate side-chains 439 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 83 optimal weight: 0.0570 chunk 31 optimal weight: 0.0020 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 146 optimal weight: 0.4980 chunk 164 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.6708 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN X 757 ASN X 769 GLN ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 597 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.080010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.067612 restraints weight = 64335.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.069646 restraints weight = 35472.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071019 restraints weight = 22365.105| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 16581 Z= 0.142 Angle : 0.771 11.385 22523 Z= 0.392 Chirality : 0.048 0.267 2577 Planarity : 0.006 0.094 2917 Dihedral : 5.715 25.945 2239 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.19 % Favored : 88.66 % Rotamer: Outliers : 0.11 % Allowed : 1.36 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.17), residues: 2055 helix: -0.93 (0.21), residues: 549 sheet: -1.58 (0.23), residues: 495 loop : -3.38 (0.18), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP X 356 HIS 0.001 0.001 HIS Z 315 PHE 0.033 0.002 PHE X 505 TYR 0.028 0.002 TYR Z 461 ARG 0.008 0.001 ARG Y 577 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 473) hydrogen bonds : angle 5.83859 ( 1332) covalent geometry : bond 0.00329 (16581) covalent geometry : angle 0.77137 (22523) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8804 (p0) cc_final: 0.8575 (p0) REVERT: X 21 GLU cc_start: 0.8515 (pp20) cc_final: 0.7935 (tm-30) REVERT: X 25 ILE cc_start: 0.8542 (tp) cc_final: 0.7935 (tp) REVERT: X 81 TRP cc_start: 0.7173 (m100) cc_final: 0.5506 (m100) REVERT: X 140 PHE cc_start: 0.7137 (t80) cc_final: 0.6745 (t80) REVERT: X 141 ILE cc_start: 0.8459 (pt) cc_final: 0.8203 (pt) REVERT: X 142 ASP cc_start: 0.5897 (m-30) cc_final: 0.5211 (m-30) REVERT: X 168 MET cc_start: 0.7873 (pmm) cc_final: 0.7630 (pmm) REVERT: X 371 LEU cc_start: 0.7542 (pt) cc_final: 0.7064 (pt) REVERT: X 375 LEU cc_start: 0.8857 (mm) cc_final: 0.8592 (mt) REVERT: X 512 ILE cc_start: 0.9203 (mm) cc_final: 0.8982 (mm) REVERT: X 527 MET cc_start: 0.7258 (mtt) cc_final: 0.6974 (mtt) REVERT: X 530 MET cc_start: 0.8866 (tpt) cc_final: 0.8601 (tpp) REVERT: X 551 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8758 (ttmt) REVERT: X 619 LEU cc_start: 0.8996 (pp) cc_final: 0.8784 (pp) REVERT: X 631 MET cc_start: 0.8493 (tpp) cc_final: 0.8135 (tpp) REVERT: X 645 ILE cc_start: 0.9254 (tp) cc_final: 0.8931 (pt) REVERT: X 658 ASP cc_start: 0.8324 (p0) cc_final: 0.8068 (p0) REVERT: X 665 GLU cc_start: 0.8789 (tm-30) cc_final: 0.8555 (tm-30) REVERT: X 666 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8526 (mtmm) REVERT: X 673 TYR cc_start: 0.8452 (m-80) cc_final: 0.8132 (m-80) REVERT: X 694 LYS cc_start: 0.8714 (tptp) cc_final: 0.8259 (tptt) REVERT: X 699 GLU cc_start: 0.8144 (mp0) cc_final: 0.7880 (mp0) REVERT: X 704 ASP cc_start: 0.8312 (t70) cc_final: 0.7975 (t0) REVERT: X 707 LYS cc_start: 0.8874 (tptp) cc_final: 0.8527 (tptp) REVERT: Y 17 ASP cc_start: 0.8818 (p0) cc_final: 0.8323 (p0) REVERT: Y 107 LEU cc_start: 0.8761 (tp) cc_final: 0.8390 (tp) REVERT: Y 220 ILE cc_start: 0.7798 (tp) cc_final: 0.7251 (pt) REVERT: Y 262 TRP cc_start: 0.9182 (m100) cc_final: 0.8951 (m100) REVERT: Y 273 ILE cc_start: 0.8470 (tp) cc_final: 0.7789 (tp) REVERT: Y 328 PHE cc_start: 0.8681 (t80) cc_final: 0.8391 (t80) REVERT: Y 337 PHE cc_start: 0.8039 (m-80) cc_final: 0.7817 (m-80) REVERT: Y 342 PHE cc_start: 0.7296 (t80) cc_final: 0.6967 (t80) REVERT: Y 380 CYS cc_start: 0.8517 (m) cc_final: 0.8068 (t) REVERT: Y 415 PHE cc_start: 0.7486 (t80) cc_final: 0.7078 (t80) REVERT: Y 519 ASP cc_start: 0.7673 (m-30) cc_final: 0.7141 (m-30) REVERT: Y 527 MET cc_start: 0.8382 (ppp) cc_final: 0.8080 (ppp) REVERT: Y 539 ASP cc_start: 0.8053 (t70) cc_final: 0.7852 (t0) REVERT: Y 547 ASN cc_start: 0.8882 (m110) cc_final: 0.8672 (m-40) REVERT: Y 619 LEU cc_start: 0.8692 (mm) cc_final: 0.8059 (tp) REVERT: Y 662 GLU cc_start: 0.8935 (pt0) cc_final: 0.8369 (pt0) REVERT: Y 673 TYR cc_start: 0.8027 (m-80) cc_final: 0.7629 (m-80) REVERT: Y 680 ASP cc_start: 0.7769 (m-30) cc_final: 0.7445 (m-30) REVERT: Y 691 PHE cc_start: 0.8827 (m-80) cc_final: 0.8120 (m-80) REVERT: Y 724 PHE cc_start: 0.6803 (m-80) cc_final: 0.5969 (m-80) REVERT: Y 726 THR cc_start: 0.8356 (p) cc_final: 0.8141 (p) REVERT: Y 732 ASP cc_start: 0.6879 (t0) cc_final: 0.6474 (t0) REVERT: Y 769 GLN cc_start: 0.7185 (mm110) cc_final: 0.6713 (tp40) REVERT: Y 773 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8125 (tm-30) REVERT: Z 5 ILE cc_start: 0.6405 (mm) cc_final: 0.5660 (mt) REVERT: Z 8 GLN cc_start: 0.7797 (pm20) cc_final: 0.7498 (pm20) REVERT: Z 21 GLU cc_start: 0.8300 (tt0) cc_final: 0.7972 (tm-30) REVERT: Z 263 LYS cc_start: 0.9243 (mppt) cc_final: 0.8911 (mmtm) REVERT: Z 271 ILE cc_start: 0.9257 (tp) cc_final: 0.8742 (tp) REVERT: Z 357 ASP cc_start: 0.8195 (m-30) cc_final: 0.7161 (m-30) REVERT: Z 425 ARG cc_start: 0.8223 (mtp85) cc_final: 0.7923 (mtp85) REVERT: Z 497 GLN cc_start: 0.7701 (mp10) cc_final: 0.7445 (mp10) REVERT: Z 514 MET cc_start: 0.7728 (mtp) cc_final: 0.7503 (mtp) REVERT: Z 611 GLN cc_start: 0.8968 (mp10) cc_final: 0.8490 (mp10) REVERT: Z 623 GLU cc_start: 0.8013 (tp30) cc_final: 0.7693 (mm-30) REVERT: Z 632 ASN cc_start: 0.8025 (t0) cc_final: 0.7502 (p0) REVERT: Z 674 ARG cc_start: 0.8967 (ptp-110) cc_final: 0.8659 (ptp90) REVERT: Z 689 LYS cc_start: 0.9152 (mmtm) cc_final: 0.8901 (mmmm) REVERT: Z 728 LYS cc_start: 0.6272 (ttpt) cc_final: 0.5887 (tppt) REVERT: Z 739 GLN cc_start: 0.8192 (tp40) cc_final: 0.7877 (tp40) REVERT: Z 748 ASP cc_start: 0.9174 (t0) cc_final: 0.8948 (t0) REVERT: Z 753 ARG cc_start: 0.8739 (tmm-80) cc_final: 0.8410 (ttp80) REVERT: Z 759 ASP cc_start: 0.8343 (p0) cc_final: 0.8040 (p0) outliers start: 2 outliers final: 0 residues processed: 503 average time/residue: 0.2881 time to fit residues: 212.3233 Evaluate side-chains 435 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 1.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 18 optimal weight: 0.0570 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 177 optimal weight: 0.0980 chunk 144 optimal weight: 0.0570 chunk 158 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN X 757 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 477 ASN Z 324 ASN Z 348 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.080754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.068157 restraints weight = 64369.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070231 restraints weight = 35543.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.071632 restraints weight = 22455.531| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16581 Z= 0.140 Angle : 0.775 11.043 22523 Z= 0.392 Chirality : 0.048 0.230 2577 Planarity : 0.006 0.083 2917 Dihedral : 5.625 25.604 2239 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.90 % Favored : 88.95 % Rotamer: Outliers : 0.16 % Allowed : 0.82 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.17), residues: 2055 helix: -0.94 (0.21), residues: 545 sheet: -1.59 (0.23), residues: 478 loop : -3.31 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP X 356 HIS 0.002 0.000 HIS Z 315 PHE 0.035 0.002 PHE X 505 TYR 0.044 0.002 TYR X 461 ARG 0.015 0.001 ARG Y 750 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 473) hydrogen bonds : angle 5.78114 ( 1332) covalent geometry : bond 0.00326 (16581) covalent geometry : angle 0.77450 (22523) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 497 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8863 (p0) cc_final: 0.8588 (p0) REVERT: X 81 TRP cc_start: 0.7157 (m100) cc_final: 0.5503 (m100) REVERT: X 140 PHE cc_start: 0.7068 (t80) cc_final: 0.6695 (t80) REVERT: X 141 ILE cc_start: 0.8453 (pt) cc_final: 0.8187 (pt) REVERT: X 142 ASP cc_start: 0.5803 (m-30) cc_final: 0.4939 (m-30) REVERT: X 168 MET cc_start: 0.7964 (pmm) cc_final: 0.7694 (pmm) REVERT: X 371 LEU cc_start: 0.7424 (pt) cc_final: 0.6988 (pt) REVERT: X 375 LEU cc_start: 0.8844 (mm) cc_final: 0.8577 (mt) REVERT: X 512 ILE cc_start: 0.9129 (mm) cc_final: 0.8897 (mm) REVERT: X 530 MET cc_start: 0.8896 (tpt) cc_final: 0.8584 (tpp) REVERT: X 551 LYS cc_start: 0.9032 (ttmt) cc_final: 0.8687 (ttpt) REVERT: X 631 MET cc_start: 0.8463 (tpp) cc_final: 0.8093 (tpp) REVERT: X 645 ILE cc_start: 0.9265 (tp) cc_final: 0.8928 (pt) REVERT: X 665 GLU cc_start: 0.8777 (tm-30) cc_final: 0.8484 (tm-30) REVERT: X 666 LYS cc_start: 0.9092 (mtmm) cc_final: 0.8488 (mtmm) REVERT: X 673 TYR cc_start: 0.8383 (m-80) cc_final: 0.8049 (m-80) REVERT: X 674 ARG cc_start: 0.7382 (tpp-160) cc_final: 0.7039 (tpp80) REVERT: X 682 PHE cc_start: 0.8601 (m-80) cc_final: 0.8292 (m-80) REVERT: X 694 LYS cc_start: 0.8782 (tptp) cc_final: 0.8360 (tptt) REVERT: X 696 ASP cc_start: 0.8890 (t0) cc_final: 0.8658 (t0) REVERT: X 699 GLU cc_start: 0.8090 (mp0) cc_final: 0.7788 (mp0) REVERT: X 704 ASP cc_start: 0.8290 (t70) cc_final: 0.7973 (t0) REVERT: X 710 ASP cc_start: 0.8153 (p0) cc_final: 0.7748 (m-30) REVERT: X 718 ILE cc_start: 0.8966 (tp) cc_final: 0.8758 (tp) REVERT: Y 4 LEU cc_start: 0.7327 (pt) cc_final: 0.6391 (pt) REVERT: Y 8 GLN cc_start: 0.8388 (mp10) cc_final: 0.7667 (mp10) REVERT: Y 9 LEU cc_start: 0.8826 (mt) cc_final: 0.8613 (mt) REVERT: Y 17 ASP cc_start: 0.8797 (p0) cc_final: 0.8326 (p0) REVERT: Y 220 ILE cc_start: 0.7626 (tp) cc_final: 0.7380 (pt) REVERT: Y 263 LYS cc_start: 0.8414 (ttpp) cc_final: 0.7808 (ttpp) REVERT: Y 265 MET cc_start: 0.8782 (mmm) cc_final: 0.8555 (mmm) REVERT: Y 273 ILE cc_start: 0.8593 (tp) cc_final: 0.7925 (tp) REVERT: Y 275 PHE cc_start: 0.8355 (t80) cc_final: 0.7941 (t80) REVERT: Y 328 PHE cc_start: 0.8671 (t80) cc_final: 0.8395 (t80) REVERT: Y 337 PHE cc_start: 0.7992 (m-80) cc_final: 0.7788 (m-80) REVERT: Y 342 PHE cc_start: 0.7423 (t80) cc_final: 0.7172 (t80) REVERT: Y 380 CYS cc_start: 0.8560 (m) cc_final: 0.7951 (t) REVERT: Y 415 PHE cc_start: 0.7421 (t80) cc_final: 0.6980 (t80) REVERT: Y 500 GLU cc_start: 0.7558 (pt0) cc_final: 0.6465 (pp20) REVERT: Y 501 LEU cc_start: 0.9320 (tp) cc_final: 0.8979 (tp) REVERT: Y 519 ASP cc_start: 0.7684 (m-30) cc_final: 0.7275 (m-30) REVERT: Y 527 MET cc_start: 0.8406 (ppp) cc_final: 0.7662 (ppp) REVERT: Y 634 ASP cc_start: 0.7934 (p0) cc_final: 0.7046 (p0) REVERT: Y 662 GLU cc_start: 0.8950 (pt0) cc_final: 0.8378 (pt0) REVERT: Y 673 TYR cc_start: 0.8122 (m-80) cc_final: 0.7847 (m-80) REVERT: Y 680 ASP cc_start: 0.7740 (m-30) cc_final: 0.7442 (m-30) REVERT: Y 691 PHE cc_start: 0.8676 (m-80) cc_final: 0.7937 (m-80) REVERT: Y 724 PHE cc_start: 0.6719 (m-80) cc_final: 0.5915 (m-80) REVERT: Y 732 ASP cc_start: 0.6900 (t0) cc_final: 0.6586 (t0) REVERT: Y 769 GLN cc_start: 0.7467 (mm110) cc_final: 0.7025 (tp40) REVERT: Y 773 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8120 (tm-30) REVERT: Z 5 ILE cc_start: 0.6109 (mm) cc_final: 0.5312 (mt) REVERT: Z 21 GLU cc_start: 0.8286 (tt0) cc_final: 0.7997 (tm-30) REVERT: Z 271 ILE cc_start: 0.9455 (tp) cc_final: 0.8829 (tp) REVERT: Z 302 GLN cc_start: 0.8315 (pp30) cc_final: 0.7919 (pp30) REVERT: Z 357 ASP cc_start: 0.8137 (m-30) cc_final: 0.7185 (m-30) REVERT: Z 371 LEU cc_start: 0.9208 (tp) cc_final: 0.8820 (tp) REVERT: Z 425 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7977 (mtp85) REVERT: Z 497 GLN cc_start: 0.7932 (mp10) cc_final: 0.7543 (mp10) REVERT: Z 514 MET cc_start: 0.7758 (mtp) cc_final: 0.7279 (mtp) REVERT: Z 525 LEU cc_start: 0.8240 (pp) cc_final: 0.7991 (pp) REVERT: Z 611 GLN cc_start: 0.8971 (mp10) cc_final: 0.8505 (mp10) REVERT: Z 632 ASN cc_start: 0.8041 (t0) cc_final: 0.7533 (p0) REVERT: Z 644 LYS cc_start: 0.8777 (mmtp) cc_final: 0.8553 (mmtp) REVERT: Z 674 ARG cc_start: 0.8884 (ptp-110) cc_final: 0.8653 (ptp90) REVERT: Z 689 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8892 (mmmm) REVERT: Z 728 LYS cc_start: 0.6278 (ttpt) cc_final: 0.5897 (tppt) REVERT: Z 753 ARG cc_start: 0.8732 (tmm-80) cc_final: 0.8409 (ttp80) REVERT: Z 759 ASP cc_start: 0.8358 (p0) cc_final: 0.8106 (p0) REVERT: Z 760 ASN cc_start: 0.7437 (m-40) cc_final: 0.6972 (m-40) REVERT: Z 764 ARG cc_start: 0.7701 (tpm170) cc_final: 0.5784 (tpm170) outliers start: 3 outliers final: 2 residues processed: 499 average time/residue: 0.2873 time to fit residues: 211.1402 Evaluate side-chains 438 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 436 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 39 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 197 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 92 optimal weight: 5.9990 chunk 115 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN X 757 ASN ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.079183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066677 restraints weight = 65190.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.068710 restraints weight = 35909.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.070083 restraints weight = 22695.192| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16581 Z= 0.168 Angle : 0.789 10.939 22523 Z= 0.405 Chirality : 0.048 0.238 2577 Planarity : 0.006 0.086 2917 Dihedral : 5.683 26.413 2239 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.39 % Favored : 88.47 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.17), residues: 2055 helix: -0.93 (0.21), residues: 549 sheet: -1.61 (0.23), residues: 476 loop : -3.32 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP X 356 HIS 0.003 0.001 HIS Z 315 PHE 0.037 0.002 PHE X 505 TYR 0.024 0.002 TYR Z 461 ARG 0.015 0.001 ARG Y 750 Details of bonding type rmsd hydrogen bonds : bond 0.04265 ( 473) hydrogen bonds : angle 5.84747 ( 1332) covalent geometry : bond 0.00389 (16581) covalent geometry : angle 0.78920 (22523) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8890 (p0) cc_final: 0.8639 (p0) REVERT: X 21 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8225 (tp30) REVERT: X 24 GLU cc_start: 0.8754 (tm-30) cc_final: 0.8493 (tm-30) REVERT: X 25 ILE cc_start: 0.8455 (tp) cc_final: 0.7978 (tp) REVERT: X 81 TRP cc_start: 0.7294 (m100) cc_final: 0.5586 (m100) REVERT: X 116 ASN cc_start: 0.8403 (t0) cc_final: 0.8058 (m-40) REVERT: X 140 PHE cc_start: 0.7152 (t80) cc_final: 0.6818 (t80) REVERT: X 141 ILE cc_start: 0.8454 (pt) cc_final: 0.8207 (pt) REVERT: X 142 ASP cc_start: 0.6219 (m-30) cc_final: 0.5430 (m-30) REVERT: X 168 MET cc_start: 0.8101 (pmm) cc_final: 0.7824 (pmm) REVERT: X 371 LEU cc_start: 0.7512 (pt) cc_final: 0.7132 (pt) REVERT: X 423 SER cc_start: 0.9139 (t) cc_final: 0.8890 (p) REVERT: X 527 MET cc_start: 0.7274 (mtt) cc_final: 0.6929 (mtt) REVERT: X 530 MET cc_start: 0.8867 (tpt) cc_final: 0.8635 (tpp) REVERT: X 551 LYS cc_start: 0.9089 (ttmt) cc_final: 0.8709 (ttpt) REVERT: X 592 THR cc_start: 0.7773 (p) cc_final: 0.7553 (p) REVERT: X 631 MET cc_start: 0.8511 (tpp) cc_final: 0.8144 (tpp) REVERT: X 644 LYS cc_start: 0.8343 (tptm) cc_final: 0.8032 (mmtt) REVERT: X 645 ILE cc_start: 0.9249 (tp) cc_final: 0.8913 (pt) REVERT: X 665 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8532 (tm-30) REVERT: X 666 LYS cc_start: 0.9105 (mtmm) cc_final: 0.8513 (mtmm) REVERT: X 673 TYR cc_start: 0.8386 (m-80) cc_final: 0.8090 (m-80) REVERT: X 694 LYS cc_start: 0.8779 (tptp) cc_final: 0.8358 (tptt) REVERT: X 696 ASP cc_start: 0.8921 (t0) cc_final: 0.8708 (t0) REVERT: X 699 GLU cc_start: 0.8106 (mp0) cc_final: 0.7822 (mp0) REVERT: X 710 ASP cc_start: 0.8152 (p0) cc_final: 0.7804 (m-30) REVERT: X 754 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8529 (tm-30) REVERT: X 768 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8421 (tm-30) REVERT: Y 4 LEU cc_start: 0.7374 (pt) cc_final: 0.6590 (pt) REVERT: Y 8 GLN cc_start: 0.8618 (mp10) cc_final: 0.7929 (mp10) REVERT: Y 17 ASP cc_start: 0.8825 (p0) cc_final: 0.8402 (p0) REVERT: Y 107 LEU cc_start: 0.8795 (tp) cc_final: 0.8447 (tp) REVERT: Y 220 ILE cc_start: 0.7801 (tp) cc_final: 0.7310 (pt) REVERT: Y 263 LYS cc_start: 0.8406 (ttpp) cc_final: 0.8046 (ttpp) REVERT: Y 275 PHE cc_start: 0.8366 (t80) cc_final: 0.7889 (t80) REVERT: Y 328 PHE cc_start: 0.8710 (t80) cc_final: 0.8394 (t80) REVERT: Y 337 PHE cc_start: 0.8001 (m-80) cc_final: 0.7786 (m-80) REVERT: Y 342 PHE cc_start: 0.7484 (t80) cc_final: 0.7255 (t80) REVERT: Y 380 CYS cc_start: 0.8523 (m) cc_final: 0.7936 (t) REVERT: Y 415 PHE cc_start: 0.7538 (t80) cc_final: 0.7115 (t80) REVERT: Y 500 GLU cc_start: 0.7486 (pt0) cc_final: 0.6449 (pp20) REVERT: Y 519 ASP cc_start: 0.7691 (m-30) cc_final: 0.7050 (m-30) REVERT: Y 527 MET cc_start: 0.8375 (ppp) cc_final: 0.7624 (ppp) REVERT: Y 634 ASP cc_start: 0.7955 (p0) cc_final: 0.7091 (p0) REVERT: Y 662 GLU cc_start: 0.8930 (pt0) cc_final: 0.8381 (pt0) REVERT: Y 673 TYR cc_start: 0.8142 (m-80) cc_final: 0.7930 (m-80) REVERT: Y 680 ASP cc_start: 0.7945 (m-30) cc_final: 0.7650 (m-30) REVERT: Y 691 PHE cc_start: 0.8748 (m-80) cc_final: 0.8028 (m-80) REVERT: Y 724 PHE cc_start: 0.6803 (m-80) cc_final: 0.6233 (m-80) REVERT: Y 729 ASN cc_start: 0.6659 (m-40) cc_final: 0.6300 (t0) REVERT: Y 732 ASP cc_start: 0.6965 (t0) cc_final: 0.6675 (t0) REVERT: Y 769 GLN cc_start: 0.7241 (mm110) cc_final: 0.6773 (tp40) REVERT: Y 773 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8138 (tm-30) REVERT: Z 5 ILE cc_start: 0.5804 (mm) cc_final: 0.5079 (mt) REVERT: Z 8 GLN cc_start: 0.7742 (pm20) cc_final: 0.7480 (pm20) REVERT: Z 21 GLU cc_start: 0.8308 (tt0) cc_final: 0.8045 (tm-30) REVERT: Z 271 ILE cc_start: 0.9409 (tp) cc_final: 0.8761 (tp) REVERT: Z 357 ASP cc_start: 0.8304 (m-30) cc_final: 0.7292 (m-30) REVERT: Z 371 LEU cc_start: 0.9244 (tp) cc_final: 0.8865 (tp) REVERT: Z 425 ARG cc_start: 0.8290 (mtp85) cc_final: 0.7857 (mtp85) REVERT: Z 497 GLN cc_start: 0.7910 (mp10) cc_final: 0.7509 (mp10) REVERT: Z 514 MET cc_start: 0.7816 (mtp) cc_final: 0.7443 (mtp) REVERT: Z 527 MET cc_start: 0.8621 (mmm) cc_final: 0.8364 (mmt) REVERT: Z 528 PHE cc_start: 0.8591 (t80) cc_final: 0.8317 (t80) REVERT: Z 544 MET cc_start: 0.8350 (mmm) cc_final: 0.8079 (mpp) REVERT: Z 611 GLN cc_start: 0.9020 (mp10) cc_final: 0.8448 (mp10) REVERT: Z 631 MET cc_start: 0.7972 (tmm) cc_final: 0.7749 (tmm) REVERT: Z 632 ASN cc_start: 0.7998 (t0) cc_final: 0.7710 (p0) REVERT: Z 659 ILE cc_start: 0.8934 (tp) cc_final: 0.8654 (tp) REVERT: Z 674 ARG cc_start: 0.8890 (ptp-110) cc_final: 0.8639 (ptp90) REVERT: Z 739 GLN cc_start: 0.8127 (tp40) cc_final: 0.7763 (tp40) REVERT: Z 759 ASP cc_start: 0.8396 (p0) cc_final: 0.8132 (p0) outliers start: 0 outliers final: 0 residues processed: 490 average time/residue: 0.3060 time to fit residues: 223.3743 Evaluate side-chains 425 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 73 optimal weight: 6.9990 chunk 189 optimal weight: 10.0000 chunk 173 optimal weight: 0.9990 chunk 38 optimal weight: 9.9990 chunk 152 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 180 optimal weight: 0.7980 chunk 169 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 221 ASN ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.064672 restraints weight = 65471.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.066678 restraints weight = 36063.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.068026 restraints weight = 22664.112| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16581 Z= 0.206 Angle : 0.815 11.390 22523 Z= 0.420 Chirality : 0.049 0.240 2577 Planarity : 0.006 0.094 2917 Dihedral : 5.867 25.666 2239 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 18.99 Ramachandran Plot: Outliers : 0.15 % Allowed : 12.31 % Favored : 87.54 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.17), residues: 2055 helix: -1.02 (0.21), residues: 549 sheet: -1.79 (0.22), residues: 517 loop : -3.34 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP X 356 HIS 0.003 0.001 HIS Z 315 PHE 0.043 0.002 PHE X 505 TYR 0.024 0.002 TYR Z 461 ARG 0.014 0.001 ARG Y 750 Details of bonding type rmsd hydrogen bonds : bond 0.04652 ( 473) hydrogen bonds : angle 5.96361 ( 1332) covalent geometry : bond 0.00471 (16581) covalent geometry : angle 0.81539 (22523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6085.78 seconds wall clock time: 107 minutes 18.79 seconds (6438.79 seconds total)